From 6ff1356e4d0916948188d0b9f7dbab336a1333fd Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 6 Nov 2024 12:24:46 +0100 Subject: [PATCH 1/9] init first unittest for workflowhub --- .github/run_unittests.yaml | 26 + sources/bin/__init__.py | 0 sources/bin/tests/readme.md | 6 + sources/bin/tests/test-data/test_tools.json | 693 +++++++++++++++ .../tests/test-data/workflowhub_api_mock.json | 806 ++++++++++++++++++ .../tests/test_extract_galaxy_workflows.py | 85 ++ sources/bin/tests/test_get_public_server.py | 35 - sources/bin/tests/test_tool_stats.py | 58 -- 8 files changed, 1616 insertions(+), 93 deletions(-) create mode 100644 .github/run_unittests.yaml create mode 100644 sources/bin/__init__.py create mode 100644 sources/bin/tests/readme.md create mode 100644 sources/bin/tests/test-data/test_tools.json create mode 100644 sources/bin/tests/test-data/workflowhub_api_mock.json create mode 100644 sources/bin/tests/test_extract_galaxy_workflows.py delete mode 100644 sources/bin/tests/test_get_public_server.py delete mode 100644 sources/bin/tests/test_tool_stats.py diff --git a/.github/run_unittests.yaml b/.github/run_unittests.yaml new file mode 100644 index 00000000..132d5adb --- /dev/null +++ b/.github/run_unittests.yaml @@ -0,0 +1,26 @@ +name: Run tests + +on: + pull_request: + branches: + - main + paths: + - 'bin/**' # This will trigger the workflow only if files in the 'bin' folder are modified. + +jobs: + unittest: + runs-on: ubuntu-20.04 + strategy: + matrix: + python-version: ['3.11'] + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install requirements + run: python -m pip install -r requirements.txt + - name: Run unittests + run: | + PYTHONPATH=bin python -m unittest discover -s bin/tests diff --git a/sources/bin/__init__.py b/sources/bin/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/sources/bin/tests/readme.md b/sources/bin/tests/readme.md new file mode 100644 index 00000000..ac40fb36 --- /dev/null +++ b/sources/bin/tests/readme.md @@ -0,0 +1,6 @@ +# Run the tests locally + +``` +cd codex/sources +PYTHONPATH=bin python -m unittest discover -s bin/tests +``` \ No newline at end of file diff --git a/sources/bin/tests/test-data/test_tools.json b/sources/bin/tests/test-data/test_tools.json new file mode 100644 index 00000000..fc2ec3bc --- /dev/null +++ b/sources/bin/tests/test-data/test_tools.json @@ -0,0 +1,693 @@ +[ + { + "Galaxy wrapper id":"abricate", + "Galaxy tool ids":[ + "abricate", + "abricate_list", + "abricate_summary" + ], + "Description":"Mass screening of contigs for antiobiotic resistance genes", + "bio.tool id":"ABRicate", + "bio.tool ids":[ + "ABRicate" + ], + "biii":null, + "bio.tool name":"ABRicate", + "bio.tool description":"Mass screening of contigs for antimicrobial resistance or virulence genes.", + "EDAM operation":[ + "Antimicrobial resistance prediction" + ], + "EDAM topic":[ + "Genomics", + "Microbiology" + ], + "Status":"Up-to-date", + "Source":"https://github.com/tseemann/abricate", + "ToolShed categories":[ + "Sequence Analysis" + ], + "ToolShed id":"abricate", + "Date of first commit of the suite":"2017-07-10", + "Galaxy wrapper owner":"iuc", + "Galaxy wrapper source":"https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/", + "Galaxy wrapper parsed folder":"https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate", + "Galaxy wrapper version":"1.0.1", + "Conda id":"abricate", + "Conda version":"1.0.1", + "EDAM operation (no superclasses)":[ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)":[ + "Genomics", + "Microbiology" + ], + "Available on UseGalaxy.org (Main)":3, + "Available on UseGalaxy.org.au":3, + "Available on UseGalaxy.eu":3, + "Available on UseGalaxy.fr":3, + "Tools available on UseGalaxy.org (Main)":3, + "Tools available on UseGalaxy.org.au":3, + "Tools available on UseGalaxy.eu":3, + "Tools available on UseGalaxy.fr":3, + "Tools available on APOSTL":0, + "Tools available on ARGs-OAP":0, + "Tools available on CIRM-CFBP":0, + "Tools available on ChemFlow":0, + "Tools available on Coloc-stats":0, + "Tools available on CropGalaxy":0, + "Tools available on Dintor":0, + "Tools available on GASLINI":0, + "Tools available on Galaxy@AuBi":3, + "Tools available on Galaxy@Pasteur":0, + "Tools available on GalaxyTrakr":3, + "Tools available on Genomic Hyperbrowser":0, + "Tools available on GigaGalaxy":0, + "Tools available on HyPhy HIV NGS Tools":0, + "Tools available on IPK Galaxy Blast Suite":0, + "Tools available on ImmPort Galaxy":0, + "Tools available on InteractoMIX":0, + "Tools available on MISSISSIPPI":0, + "Tools available on Mandoiu Lab":0, + "Tools available on MiModD NacreousMap":0, + "Tools available on Oqtans":0, + "Tools available on Palfinder":0, + "Tools available on PepSimili":0, + "Tools available on PhagePromotor":0, + "Tools available on UseGalaxy.be":2, + "Tools available on UseGalaxy.cz":3, + "Tools available on UseGalaxy.no":3, + "Tools available on Viral Variant Visualizer (VVV)":0, + "No. of tool users (5 years) (usegalaxy.eu)":619817, + "No. of tool users (all time) (usegalaxy.eu)":622353, + "Tool usage (5 years) (usegalaxy.eu)":4097, + "Tool usage (all time) (usegalaxy.eu)":4130, + "No. of tool users (5 years) (usegalaxy.org)":320454, + "No. of tool users (all time) (usegalaxy.org)":320454, + "Tool usage (5 years) (usegalaxy.org)":2915, + "Tool usage (all time) (usegalaxy.org)":2915, + "No. of tool users (5 years) (usegalaxy.org.au)":496156, + "No. of tool users (all time) (usegalaxy.org.au)":503743, + "Tool usage (5 years) (usegalaxy.org.au)":2012, + "Tool usage (all time) (usegalaxy.org.au)":2227, + "No. of tool users (5 years) - 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Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Genomics", + "Microbiology", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/shovill", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "shovill", + "Date of first commit of the suite": "2017-10-24", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", + "Galaxy wrapper version": "1.1.0", + "Conda id": "shovill", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Microbiology", + "Sequence assembly" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1, + "Tools available on Viral Variant Visualizer (VVV)": 0, + "No. of tool users (5 years) (usegalaxy.eu)": 46125, + "No. of tool users (all time) (usegalaxy.eu)": 47376, + "Tool usage (5 years) (usegalaxy.eu)": 2273, + "Tool usage (all time) (usegalaxy.eu)": 2356, + "No. of tool users (5 years) (usegalaxy.org)": 40577, + "No. of tool users (all time) (usegalaxy.org)": 40577, + "Tool usage (5 years) (usegalaxy.org)": 3971, + "Tool usage (all time) (usegalaxy.org)": 3971, + "No. of tool users (5 years) (usegalaxy.org.au)": 19960, + "No. of tool users (all time) (usegalaxy.org.au)": 21130, + "Tool usage (5 years) (usegalaxy.org.au)": 1085, + "Tool usage (all time) (usegalaxy.org.au)": 1199, + "No. of tool users (5 years) - all main servers": 106662, + "No. of tool users (all time) - all main servers": 109083, + "Tool usage (5 years) - all main servers": 7329, + "Tool usage (all time) - all main servers": 7526 + } + ] \ No newline at end of file diff --git a/sources/bin/tests/test-data/workflowhub_api_mock.json b/sources/bin/tests/test-data/workflowhub_api_mock.json new file mode 100644 index 00000000..214d6789 --- /dev/null +++ b/sources/bin/tests/test-data/workflowhub_api_mock.json @@ -0,0 +1,806 @@ +[ + { + "data":[ + { + "id":"1189", + "type":"workflows", + "attributes":{ + "title":"AMR-Pathfinder", + "tags":[ + "bioinformatics" + ] + }, + "links":{ + "self":"/workflows/1189" + } + }, + { + "id":"1190", + "type":"workflows", + "attributes":{ + "title":"haploid-variant-calling-wgs-pe/main", + "tags":[ + "genomics" + ] + }, + "links":{ + "self":"/workflows/1190" + } + } + ] + }, + { + "data":{ + "id":"1189", + "type":"workflows", + "attributes":{ + "discussion_links":[ + + ], + "title":"AMR-Pathfinder", + "license":"MIT", + "description":"This is an aggregation of the work done in [Seq4AMR](https://workflowhub.eu/projects/110) consisting of the following workflows:\r\n\r\n- [WF1: AbritAMR / AMRFinderPlus](https://workflowhub.eu/workflows/634)\r\n- [WF2: Sciensano](https://workflowhub.eu/workflows/644) (**not currently included**)\r\n- [WF3: SRST2](https://workflowhub.eu/workflows/407) \r\n- [WF4: StarAMR](https://workflowhub.eu/workflows/470)\r\n\r\n## Installation\r\n\r\n- You will need to:\r\n - run the [RGI Database Builder](https://my.galaxy.training/?path=?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcard%2Frgi%2Frgi_database_builder%2F1.2.0) as a Galaxy admin (if this hasn\\'t been done already)\r\n - [Have the en_US.UTF-8 locale installed](https://github.com/galaxyproject/tools-iuc/issues/6467) on the compute nodes executing cast/melt jobs.\r\n - Install the requisite tools with e.g. [`shed-tools`](https://ephemeris.readthedocs.io/en/latest/commands/shed-tools.html) command from the [`ephemeris`](https://ephemeris.readthedocs.io/en/latest/) suite: `shed-tools install -g https://galaxy.example.com -a API_KEY -t tools.yaml` (tools.yaml is provided in this repository.)\r\n- Then you can import this workflow\r\n - Navigate to `/workflows/import` of your Galaxy server\r\n - Select \"GA4GH servers\"\r\n - Enter `name:\"AMR-Pathfinder\"`\r\n- And run it\r\n - You must provide a Sequencing collection (list:paired of fastq files)\r\n - And a Genomes collection (list of fasta files) \r\n - Both of these should use **identical** collection element identifiers\r\n\r\n## Outputs\r\n\r\nThis will produce two important tables: \"Binary Comparison\" and a \"% Identity Scored Outputs\". \r\n\r\n### Binary comparison\r\n\r\nThis file reports the discovery or absence of specific AMR genes across all tested AMR Analysis tools. You will mostly see 1s (presence) or 0s (absence) but you may occasionally see higher numbers when an AMR tool reports multiple hits for a specific gene.\r\n\r\n### % Identity Scored Outputs\r\n\r\nThis is similar to binary comparison, but using the % identity reported by each AMR tool. For cases where multiple hits were detected, we take the highest.\r\n\r\n## Known Issues\r\n\r\nThe names for identified AMR genes is highly inconsistent across AMR analysis tools. We urge the AMR community to rectify this by standardising gene names used in their tooling.", + "latest_version":1, + "tags":[ + "AMR", + "AMR-detection", + "benchamrking" + ], + "versions":[ + { + "version":1, + "revision_comments":"Initial working version of the AMR Pathfinder project workflow", + "url":"https://workflowhub.eu/workflows/1189?version=1", + "commit":"a29814deaf5d824562481df6357ff3c89295c5b0", + "ref":"refs/tags/Version-4.6", + "tree":"/workflows/1189/git/1/tree", + "doi":"10.48546/workflowhub.workflow.1189.1" + } + ], + "version":1, + "revision_comments":"Initial working version of the AMR Pathfinder project workflow", + "created_at":"2024-10-28T13:43:16.000Z", + "updated_at":"2024-11-04T16:21:43.000Z", + "doi":"10.48546/workflowhub.workflow.1189.1", + "content_blobs":[ + + ], + "creators":[ + { + "profile":"/people/118", + "family_name":"Rasche", + "given_name":"Helena", + "affiliation":"", + "orcid":"https://orcid.org/0000-0001-9760-8992" + }, + { + "profile":"/people/359", + "family_name":"Dollée", + "given_name":"Dennis", + "affiliation":"Erasmus University Medical Centre", + "orcid":"None" + }, + { + "profile":"/people/875", + "family_name":"Rijvers", + "given_name":"Birgit", + "affiliation":"Erasmus University Medical Centre", + "orcid":"None" + } + ], + "other_creators":"", + "workflow_class":{ + "title":"Galaxy", + "key":"galaxy", + "description":"None" + }, + "operation_annotations":[ + { + "label":"Antimicrobial resistance prediction", + "identifier":"http://edamontology.org/operation_3482" + } + ], + "topic_annotations":[ + + ], + "internals":{ + "steps":[ + { + "id":"5", + "name":"Create text file", + "description":"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0" + }, + { + "id":"6", + "name":"Sanitize Filename", + "description":"" + }, + { + "id":"7", + "name":"Shovill", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1" + }, + { + "id":"8", + "name":"WF3: SRST2 :: AMR - SeqSero2/SISTR", + "description":"" + }, + { + "id":"9", + "name":"Replace", + "description":"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4" + }, + { + "id":"10", + "name":"benchAMRking: wf1", + "description":"" + }, + { + "id":"11", + "name":"benchAMRking: wf3b", + "description":"" + }, + { + "id":"12", + "name":"ABRicate", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1" + }, + { + "id":"13", + "name":"staramr", + "description":"toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1" + }, + { + "id":"14", + "name":"Add column", + "description":"addValue" + }, + { + "id":"15", + "name":"Add column", + "description":"addValue" + }, + { + "id":"16", + "name":"Add column", + "description":"addValue" + }, + { + "id":"17", + "name":"hamronize", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1" + }, + { + "id":"18", + "name":"hamronize", + 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"description":"toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0" + }, + { + "id":"36", + "name":"Add column", + "description":"addValue" + }, + { + "id":"37", + "name":"Concatenate datasets", + "description":"cat1" + }, + { + "id":"38", + "name":"Concatenate datasets", + "description":"cat1" + }, + { + "id":"39", + "name":"% Identity", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2" + }, + { + "id":"40", + "name":"Binary Comparison", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2" + } + ] + }, + "tools":[ + { + "name":"shovill", + "id":"https://bio.tools/shovill" + }, + { + "name":"ABRicate", + "id":"https://bio.tools/ABRicate" + }, + { + "name":"staramr", + "id":"https://bio.tools/staramr" + }, + { + "name":"hAMRonization", + "id":"https://bio.tools/hamronization" + } + ] + }, + "relationships":{ + "creators":{ + "data":[ + { + "id":"118", + "type":"people" + }, + { + "id":"359", + "type":"people" + }, + { + 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"uuid":"81fea0b0-7760-013d-5d70-005056ab8eb2" + } + }, + "jsonapi":{ + "version":"1.0" + } + }, + { + "data":{ + "id":"1189", + "type":"workflows", + "attributes":{ + "discussion_links":[ + + ], + "title":"AMR-Pathfinder", + "license":"MIT", + "description":"This is an aggregation of the work done in [Seq4AMR](https://workflowhub.eu/projects/110) consisting of the following workflows:\r\n\r\n- [WF1: AbritAMR / AMRFinderPlus](https://workflowhub.eu/workflows/634)\r\n- [WF2: Sciensano](https://workflowhub.eu/workflows/644) (**not currently included**)\r\n- [WF3: SRST2](https://workflowhub.eu/workflows/407) \r\n- [WF4: StarAMR](https://workflowhub.eu/workflows/470)\r\n\r\n## Installation\r\n\r\n- You will need to:\r\n - run the [RGI Database Builder](https://my.galaxy.training/?path=?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fcard%2Frgi%2Frgi_database_builder%2F1.2.0) as a Galaxy admin (if this hasn\\'t been done already)\r\n - [Have the en_US.UTF-8 locale installed](https://github.com/galaxyproject/tools-iuc/issues/6467) on the compute nodes executing cast/melt jobs.\r\n - Install the requisite tools with e.g. [`shed-tools`](https://ephemeris.readthedocs.io/en/latest/commands/shed-tools.html) command from the [`ephemeris`](https://ephemeris.readthedocs.io/en/latest/) suite: `shed-tools install -g https://galaxy.example.com -a API_KEY -t tools.yaml` (tools.yaml is provided in this repository.)\r\n- Then you can import this workflow\r\n - Navigate to `/workflows/import` of your Galaxy server\r\n - Select \"GA4GH servers\"\r\n - Enter `name:\"AMR-Pathfinder\"`\r\n- And run it\r\n - You must provide a Sequencing collection (list:paired of fastq files)\r\n - And a Genomes collection (list of fasta files) \r\n - Both of these should use **identical** collection element identifiers\r\n\r\n## Outputs\r\n\r\nThis will produce two important tables: \"Binary Comparison\" and a \"% Identity Scored Outputs\". \r\n\r\n### Binary comparison\r\n\r\nThis file reports the discovery or absence of specific AMR genes across all tested AMR Analysis tools. You will mostly see 1s (presence) or 0s (absence) but you may occasionally see higher numbers when an AMR tool reports multiple hits for a specific gene.\r\n\r\n### % Identity Scored Outputs\r\n\r\nThis is similar to binary comparison, but using the % identity reported by each AMR tool. For cases where multiple hits were detected, we take the highest.\r\n\r\n## Known Issues\r\n\r\nThe names for identified AMR genes is highly inconsistent across AMR analysis tools. We urge the AMR community to rectify this by standardising gene names used in their tooling.", + "latest_version":1, + "tags":[ + "AMR", + "AMR-detection", + "benchamrking" + ], + "versions":[ + { + "version":1, + "revision_comments":"Initial working version of the AMR Pathfinder project workflow", + "url":"https://workflowhub.eu/workflows/1189?version=1", + "commit":"a29814deaf5d824562481df6357ff3c89295c5b0", + "ref":"refs/tags/Version-4.6", + "tree":"/workflows/1189/git/1/tree", + "doi":"10.48546/workflowhub.workflow.1189.1" + } + ], + "version":1, + "revision_comments":"Initial working version of the AMR Pathfinder project workflow", + "created_at":"2024-10-28T13:43:16.000Z", + "updated_at":"2024-11-04T16:21:43.000Z", + "doi":"10.48546/workflowhub.workflow.1189.1", + "content_blobs":[ + + ], + "creators":[ + { + "profile":"/people/118", + "family_name":"Rasche", + "given_name":"Helena", + "affiliation":"", + "orcid":"https://orcid.org/0000-0001-9760-8992" + }, + { + "profile":"/people/359", + "family_name":"Dollée", + "given_name":"Dennis", + "affiliation":"Erasmus University Medical Centre", + "orcid":"None" + }, + { + "profile":"/people/875", + "family_name":"Rijvers", + "given_name":"Birgit", + "affiliation":"Erasmus University Medical Centre", + "orcid":"None" + } + ], + "other_creators":"", + "workflow_class":{ + "title":"Galaxy", + "key":"galaxy", + "description":"None" + }, + "operation_annotations":[ + { + "label":"Antimicrobial resistance prediction", + "identifier":"http://edamontology.org/operation_3482" + } + ], + "topic_annotations":[ + + ], + "internals":{ + "steps":[ + { + "id":"5", + "name":"Create text file", + "description":"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0" + }, + { + "id":"6", + "name":"Sanitize Filename", + "description":"" + }, + { + "id":"7", + "name":"Shovill", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1" + }, + { + "id":"8", + "name":"WF3: SRST2 :: AMR - SeqSero2/SISTR", + "description":"" + }, + { + "id":"9", + "name":"Replace", + "description":"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4" + }, + { + "id":"10", + "name":"benchAMRking: wf1", + "description":"" + }, + { + "id":"11", + "name":"benchAMRking: wf3b", + "description":"" + }, + { + "id":"12", + "name":"ABRicate", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1" + }, + { + "id":"13", + "name":"staramr", + "description":"toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1" + }, + { + "id":"14", + "name":"Add column", + "description":"addValue" + }, + { + "id":"15", + "name":"Add column", + "description":"addValue" + }, + { + "id":"16", + "name":"Add column", + "description":"addValue" + }, + { + "id":"17", + "name":"hamronize", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1" + }, + { + "id":"18", + "name":"hamronize", + 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{ + "id":"26", + "name":"Split file", + "description":"toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2" + }, + { + "id":"27", + "name":"Cut", + "description":"Cut1" + }, + { + "id":"28", + "name":"Select", + "description":"Grep1" + }, + { + "id":"29", + "name":"Add column", + "description":"addValue" + }, + { + "id":"30", + "name":"Merge collections", + "description":"__MERGE_COLLECTION__" + }, + { + "id":"31", + "name":"Apply rules", + "description":"__APPLY_RULES__" + }, + { + "id":"32", + "name":"Concatenate multiple datasets", + "description":"toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3" + }, + { + "id":"33", + "name":"Move WF# col to second position, keep score", + "description":"Cut1" + }, + { + "id":"34", + "name":"Move WF# col to second position 2, delete score", + "description":"Cut1" + }, + { + "id":"35", + "name":"Datamash", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0" + }, + { + "id":"36", + "name":"Add column", + "description":"addValue" + }, + { + "id":"37", + "name":"Concatenate datasets", + "description":"cat1" + }, + { + "id":"38", + "name":"Concatenate datasets", + "description":"cat1" + }, + { + "id":"39", + "name":"% Identity", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2" + }, + { + "id":"40", + "name":"Binary Comparison", + "description":"toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2" + } + ] + }, + "tools":[ + { + "name":"shovill", + "id":"https://bio.tools/shovill" + }, + { + "name":"ABRicate", + "id":"https://bio.tools/ABRicate" + }, + { + "name":"staramr", + "id":"https://bio.tools/staramr" + }, + { + "name":"hAMRonization", + "id":"https://bio.tools/hamronization" + } + ] + }, + "relationships":{ + "creators":{ + "data":[ + { + "id":"118", + "type":"people" + }, + { + "id":"359", + "type":"people" + }, + { + "id":"875", + "type":"people" + } + ] + }, + "submitter":{ + "data":[ + { + "id":"118", + "type":"people" + } + ] + }, + "people":{ + "data":[ + { + "id":"118", + "type":"people" + }, + { + "id":"359", + "type":"people" + }, + { + "id":"875", + "type":"people" + } + ] + }, + "projects":{ + "data":[ + { + "id":"110", + "type":"projects" + }, + { + "id":"277", + "type":"projects" + } + ] + }, + "investigations":{ + "data":[ + + ] + }, + "studies":{ + "data":[ + + ] + }, + "assays":{ + "data":[ + + ] + }, + "publications":{ + "data":[ + + ] + }, + "sops":{ + "data":[ + + ] + }, + "presentations":{ + "data":[ + + ] + }, + "data_files":{ + "data":[ + + ] + }, + "documents":{ + "data":[ + + ] + } + }, + "links":{ + "self":"/workflows/1189?version=1", + "diagram":"/workflows/1189/diagram?version=1" + }, + "meta":{ + "created":"2024-10-28T13:43:16.000Z", + "modified":"2024-11-04T15:04:22.000Z", + "api_version":"0.3", + "base_url":"https://workflowhub.eu", + "uuid":"81fea0b0-7760-013d-5d70-005056ab8eb2" + } + }, + "jsonapi":{ + "version":"1.0" + } + } + ] \ No newline at end of file diff --git a/sources/bin/tests/test_extract_galaxy_workflows.py b/sources/bin/tests/test_extract_galaxy_workflows.py new file mode 100644 index 00000000..c35b5974 --- /dev/null +++ b/sources/bin/tests/test_extract_galaxy_workflows.py @@ -0,0 +1,85 @@ +import json +import os +import unittest +from typing import ( + Any, + Dict, +) +from unittest.mock import ( + MagicMock, + patch, +) + +from bin.extract_galaxy_workflows import Workflows + +from bin import shared + + +class TestAddWorkflowsFromWorkflowHub(unittest.TestCase): + + def setUp(self) -> None: + """Set up the test environment and prepare mock data.""" + # Get the directory where the script is located + self.script_dir = os.path.dirname(os.path.realpath(__file__)) + + # Construct the path to the JSON file (relative to the script's location) + json_file_path = os.path.join(self.script_dir, "test-data", "workflowhub_api_mock.json") + + # Open and load the JSON file + with open(json_file_path, "r") as file: + self.mock_responses = json.load(file) + + # Define the side effect function + def mock_side_effect(url: str, headers: Dict[str, str]) -> Dict: + if url == "https://workflowhub.eu/workflows?filter[workflow_type]=galaxy": + return self.mock_responses[0] + elif url == "https://workflowhub.eu/workflows/1189": + return self.mock_responses[1] + elif url == "https://workflowhub.eu/workflows/1190": + return self.mock_responses[2] + else: + return {"data": []} # Default empty response for any other URL + + self.mock_side_effect = mock_side_effect # Store for reuse in tests + + # Construct the path to the JSON file (relative to the script's location) + self.test_tools_file_path = os.path.join(self.script_dir, "test-data", "test_tools.json") + + @patch("shared.get_request_json") + def test_add_workflows_from_workflowhub(self, mock_get_request_json: MagicMock) -> None: + + # Mock the first call to get_request_json to return the mock list response + mock_get_request_json.side_effect = self.mock_side_effect + + # Create the Workflows instance and invoke the method + workflows_instance = Workflows(test=True) # Set test=True to limit data processed + workflows_instance.tools = shared.read_suite_per_tool_id(self.test_tools_file_path) + workflows_instance.add_workflows_from_workflowhub() + + # Assert that the correct number of workflows were added + self.assertEqual(len(workflows_instance.workflows), 2) # Should have added all 6 workflows + + # Check details of the first added workflow as an example + first_workflow = workflows_instance.workflows[0] + self.assertEqual(first_workflow.id, "1189") + self.assertEqual(first_workflow.name, "AMR-Pathfinder") + self.assertEqual(first_workflow.link, "https://workflowhub.eu/workflows/1189?version=1") + + # Optionally check that the mock was called with the expected URLs + mock_get_request_json.assert_any_call( + "https://workflowhub.eu/workflows?filter[workflow_type]=galaxy", {"Accept": "application/json"} + ) + mock_get_request_json.assert_any_call("https://workflowhub.eu/workflows/1189", {"Accept": "application/json"}) + mock_get_request_json.assert_any_call("https://workflowhub.eu/workflows/1190", {"Accept": "application/json"}) + + self.assertEqual(mock_get_request_json.call_count, 3) # Adjust based on the expected number of calls + + # check if edam terms are transferred from the tools to the workflow + self.assertEqual( + set(first_workflow.edam_operation), set(["Antimicrobial resistance prediction", "Genome assembly"]) + ) + + +# Run the tests +if __name__ == "__main__": + unittest.main() diff --git a/sources/bin/tests/test_get_public_server.py b/sources/bin/tests/test_get_public_server.py deleted file mode 100644 index a78f3225..00000000 --- a/sources/bin/tests/test_get_public_server.py +++ /dev/null @@ -1,35 +0,0 @@ -###################################### -# Initial start for function based unit tests -# need to set this up using a proper testing framework -###################################### - -import os -import sys - -sys.path.append(os.path.dirname(os.path.dirname(os.path.realpath(__file__)))) - -from extract_galaxy_tools import ( - check_tools_on_servers, - USEGALAXY_SERVER_URLS, -) - -server_url = USEGALAXY_SERVER_URLS["UseGalaxy.eu"] -tool_ids = ["abricate"] - -count = check_tools_on_servers(tool_ids, server_url) -print(count) - -tool_ids = ["bla"] -count = check_tools_on_servers(tool_ids, server_url) -print(count) - -server_url = "https://jolo.eu" -tool_ids = ["bla"] -count = check_tools_on_servers(tool_ids, server_url) -print(count) - -# test the cache ! -server_url = "https://jolo.eu" -tool_ids = ["bla", "blub"] -count = check_tools_on_servers(tool_ids, server_url) -print(count) diff --git a/sources/bin/tests/test_tool_stats.py b/sources/bin/tests/test_tool_stats.py deleted file mode 100644 index 86f29b12..00000000 --- a/sources/bin/tests/test_tool_stats.py +++ /dev/null @@ -1,58 +0,0 @@ -import os -import sys -from typing import List - -import pandas as pd - -sys.path.append(os.path.dirname(os.path.dirname(os.path.realpath(__file__)))) - -from extract_galaxy_tools import GALAXY_TOOL_STATS - - -def get_last_url_position(toot_id: str) -> str: - """ - Returns the last url position of the toot_id, if the value is not a - url it returns the toot_id. So works for local and toolshed - installed tools. - - :param tool_id: galaxy tool id - """ - - if "/" in toot_id: - toot_id = toot_id.split("/")[-1] - return toot_id - - -def get_tool_stats_from_stats_file(tool_stats_df: pd.DataFrame, tool_ids: List[str]) -> int: - """ - Adds the usage statistics to the community tool table - - :param tools_stats_df: df with tools stats in the form `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter,3394539` - :tool_ids: tool ids to get statistics for and aggregate - """ - - # extract tool id - tool_stats_df["Galaxy wrapper id"] = tool_stats_df["tool_name"].apply(get_last_url_position) - # print(tool_stats_df["Galaxy wrapper id"].to_list()) - - agg_count = 0 - for tool_id in tool_ids: - if tool_id in tool_stats_df["Galaxy wrapper id"].to_list(): - - # get stats of the tool for all versions - counts = tool_stats_df.loc[(tool_stats_df["Galaxy wrapper id"] == tool_id), "count"] - agg_versions = counts.sum() - - # aggregate all counts for all tools in the suite - agg_count += agg_versions - - return int(agg_count) - - -tools_stats_df = pd.read_csv(GALAXY_TOOL_STATS["Total tool usage (usegalaxy.eu)"]) - -tool_ids = ["nextclade"] - -counts = get_tool_stats_from_stats_file(tools_stats_df, tool_ids) - -print(counts) From 00f1ba19732d5fc683add8eb884a85d8735c5d8d Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 6 Nov 2024 14:11:11 +0100 Subject: [PATCH 2/9] move unittest CI --- .github/{ => workflows}/run_unittests.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/{ => workflows}/run_unittests.yaml (100%) diff --git a/.github/run_unittests.yaml b/.github/workflows/run_unittests.yaml similarity index 100% rename from .github/run_unittests.yaml rename to .github/workflows/run_unittests.yaml From 0c0a0cf332569bf35bf79f0f1d08c0d6df08d24a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Tue, 5 Nov 2024 09:27:05 +0100 Subject: [PATCH 3/9] Modify spoc TS cat and add tool status --- communities/spoc/metadata/categories | 1 + communities/spoc/metadata/tool_status.tsv | 100 + communities/spoc/resources/tools.html | 3462 ++++++++++++++++- communities/spoc/resources/tools.tsv | 76 +- .../tools_filtered_by_ts_categories.tsv | 123 +- .../spoc/resources/tools_wordcloud.png | Bin 124156 -> 151440 bytes 6 files changed, 3575 insertions(+), 187 deletions(-) create mode 100644 communities/spoc/metadata/tool_status.tsv diff --git a/communities/spoc/metadata/categories b/communities/spoc/metadata/categories index b76ed2c4..a86034b3 100644 --- a/communities/spoc/metadata/categories +++ b/communities/spoc/metadata/categories @@ -1,2 +1,3 @@ Single Cell Spatial Omics +Transcriptomics \ No newline at end of file diff --git a/communities/spoc/metadata/tool_status.tsv b/communities/spoc/metadata/tool_status.tsv new file mode 100644 index 00000000..7faf75ee --- /dev/null +++ b/communities/spoc/metadata/tool_status.tsv @@ -0,0 +1,100 @@ +aegean FALSE FALSE +anndata TRUE FALSE +arriba FALSE FALSE +askor FALSE FALSE +bamparse FALSE FALSE +baredsc TRUE FALSE +bctools FALSE FALSE +brew3r_r FALSE FALSE +cell-types-analysis TRUE FALSE +cemitool TRUE FALSE +cherri FALSE FALSE +chira FALSE FALSE +cite_seq_count TRUE FALSE +cosg TRUE FALSE +cpat FALSE FALSE +cpm_tpm_rpk FALSE FALSE +crosscontamination_barcode_filter TRUE FALSE +cuffcompare FALSE FALSE +cuffdiff FALSE FALSE +cufflinks FALSE FALSE +cuffmerge FALSE FALSE +cuffnorm FALSE FALSE +cuffquant FALSE FALSE +data-hca TRUE FALSE +data-scxa TRUE FALSE +decoupler TRUE FALSE +deg_annotate TRUE FALSE +deseq2 TRUE FALSE +deseq2_normalization TRUE FALSE +dexseq TRUE FALSE +dropletutils TRUE FALSE +edger TRUE FALSE +egsea TRUE FALSE +episcanpy TRUE FALSE +fastq_provider FALSE FALSE +fastq_utils FALSE FALSE +featurecounts FALSE FALSE +fgsea TRUE FALSE +garnett TRUE FALSE +genomic_super_signature FALSE FALSE +gffcompare FALSE FALSE +gsc_filter_cells TRUE FALSE +gsc_filter_genes TRUE FALSE +gsc_gene_expression_correlations TRUE FALSE +gsc_high_dimensions_visualisation TRUE FALSE +gsc_mannwhitney_de TRUE FALSE +gsc_scran_normalize TRUE FALSE +gsc_signature_score TRUE FALSE +heinz TRUE FALSE +infercnv TRUE FALSE +isoformswitchanalyzer FALSE FALSE +kallisto FALSE FALSE +limma_voom FALSE FALSE +masigpro FALSE FALSE +mircounts FALSE FALSE +monocle3 TRUE FALSE +multigsea TRUE FALSE +music_deconvolution TRUE FALSE +nugen_nudup FALSE FALSE +pathifier FALSE FALSE +pizzly FALSE FALSE +psiclass FALSE FALSE +pyscenic TRUE FALSE +qualimap FALSE FALSE +raceid TRUE FALSE +repenrich FALSE FALSE +repenrich2 FALSE FALSE +rgrnastar TRUE FALSE +ribowaltz FALSE FALSE +rsem FALSE FALSE +rseqc FALSE FALSE +ruvseq FALSE FALSE +salmon TRUE FALSE +sashimi_plot FALSE FALSE +sc3 TRUE FALSE +scanpy TRUE FALSE +scater TRUE FALSE +sccaf TRUE FALSE +sceasy TRUE FALSE +schicexplorer TRUE FALSE +scmap TRUE FALSE +scpipe TRUE FALSE +scpred TRUE FALSE +seurat TRUE FALSE +sinto TRUE FALSE +slamdunk FALSE FALSE +sleuth FALSE FALSE +snapatac2 TRUE FALSE +spapros TRUE FALSE +star_fusion FALSE FALSE +stringtie FALSE FALSE +tophat_fusion_post FALSE FALSE +transdecoder FALSE FALSE +trinity FALSE FALSE +trinotate FALSE FALSE +tximport FALSE FALSE +ucsc-cell-browser TRUE FALSE +umi_tools TRUE FALSE +velocyto TRUE FALSE +volcanoplot TRUE FALSE \ No newline at end of file diff --git a/communities/spoc/resources/tools.html b/communities/spoc/resources/tools.html index fee090cf..2e8c7922 100644 --- a/communities/spoc/resources/tools.html +++ b/communities/spoc/resources/tools.html @@ -213,7 +213,7 @@ 69688 3002 3003 - + False @@ -292,7 +292,165 @@ 161 22 22 + False + + + + cell-types-analysis + ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals + Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis + + + + + + + + To update + + Transcriptomics, RNA, Statistics + suite_cell_types_analysis + 2020-04-07 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis + 1.1.1 + cell-types-analysis + 0.1.11 + + + 0 + 0 + 6 + 0 + 0 + 0 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 8 + 8 + 4 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 8 + 8 + 4 + 4 + False + + + + cemitool + cemitool + Gene co-expression network analysis tool + cemitool + cemitool + CEMiTool + It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + Enrichment analysis, Pathway or network analysis + Gene expression, Transcriptomics, Microarray experiment + Up-to-date + https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html + Transcriptomics, RNA, Statistics + cemitool + 2022-10-10 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool + 1.26.0 + bioconductor-cemitool + 1.26.0 + Enrichment analysis, Pathway or network analysis + Transcriptomics, Microarray experiment + 1 + 0 + 1 + 0 + 1 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 225 + 225 + 32 + 32 + 271 + 271 + 61 + 61 + 0 + 0 + 0 + 0 + 496 + 496 + 93 + 93 + False @@ -371,7 +529,7 @@ 48 10 10 - + False @@ -450,40 +608,39 @@ 0 0 0 - + False - dropletutils - dropletutils - DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data - dropletutils - dropletutils + crosscontamination_barcode_filter + crosscontamination_barcode_filter + Barcode contamination discovery tool + + + + + + - DropletUtils - Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. - Loading, Community profiling - Gene expression, RNA-seq, Sequencing, Transcriptomics To update - https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html - Single Cell, Sequence Analysis - dropletutils - 2019-09-02 + + Transcriptomics, Visualization + crosscontamination_barcode_filter + 2018-07-27 iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ - https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils - 1.10.0 - bioconductor-dropletutils - 1.22.0 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter + https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter + 0.3 + r-ggplot2 + 2.2.1 + - Sequencing, Transcriptomics - 1 - 1 - 1 - 1 1 + 0 1 + 0 1 + 0 1 0 0 @@ -498,7 +655,8 @@ 0 0 0 - 1 + 0 + 0 0 0 0 @@ -513,60 +671,56 @@ 1 1 0 - 4413 - 4442 - 430 - 431 - 4403 - 4403 - 255 - 255 - 1816 - 1816 - 33 - 33 - 10632 - 10661 - 718 - 719 - + 276 + 390 + 61 + 76 + 131 + 131 + 42 + 42 + 0 + 0 + 0 + 0 + 407 + 521 + 103 + 118 + False - episcanpy - episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess - EpiScanpy – Epigenomics single cell analysis in python - episcanpy - episcanpy + data-hca + hca_matrix_downloader + Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects + + + + + + - epiScanpy - Epigenomics Single Cell Analysis in Python. - Enrichment analysis, Imputation - Epigenomics, Cell biology, DNA To update - https://github.com/colomemaria/epiScanpy - Single Cell, Epigenetics - episcanpy - 2023-03-22 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ - https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy - 0.3.2 - episcanpy - 0.4.0 - Enrichment analysis, Imputation - Epigenomics, Cell biology, DNA - 3 - 3 - 3 + + Transcriptomics, Sequence Analysis + suite_human_cell_atlas_tools + 2019-07-02 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca + v0.0.4+galaxy0 + hca-matrix-downloader + 0.0.4 + + 0 - 3 - 3 - 3 0 + 1 0 0 0 + 1 0 0 0 @@ -589,32 +743,36 @@ 0 0 0 - 3 0 0 - 880 - 880 - 80 - 80 - 221 - 221 - 37 - 37 - 49 - 49 + 0 + 0 + 1 + 1 + 0 + 441 + 451 + 83 + 87 3 3 - 1150 - 1150 - 120 - 120 - + 2 + 2 + 0 + 0 + 0 + 0 + 444 + 454 + 85 + 89 + False - raceid - raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory - RaceID3, StemID2, FateID - scRNA analysis + data-scxa + retrieve_scxa + Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home @@ -623,21 +781,2075 @@ To update - https://github.com/dgrun/RaceID3_StemID2_package/ - Single Cell, Transcriptomics - 2021-04-14 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid - 0.2.3 - r-raceid - 0.1.3 + Transcriptomics, Sequence Analysis + suite_ebi_expression_atlas + 2019-07-02 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa + v0.0.2+galaxy2 + wget + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 0 + 867 + 877 + 213 + 216 + 339 + 339 + 94 + 94 + 64 + 64 + 5 + 5 + 1270 + 1280 + 312 + 315 + False + + + + decoupler + score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk + decoupler - Ensemble of methods to infer biological activities + + + + + + + + To update + https://decoupler-py.readthedocs.io/en/latest/ + Transcriptomics + suite_decoupler + 2023-09-24 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler + 1.4.0+galaxy3 + decoupler + 1.5.0 + + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 54 + 54 + 6 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 54 + 54 + 6 + 6 + False + + + + deg_annotate + deg_annotate + Annotate DESeq2/DEXSeq output tables + + + + + + + + To update + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + Transcriptomics + deg_annotate + 2018-11-22 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate + 1.1.0 + bedtools + 2.31.1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 22774 + 23146 + 4084 + 4155 + 33972 + 33972 + 5372 + 5372 + 4236 + 4236 + 846 + 846 + 60982 + 61354 + 10302 + 10373 + False + + + + deseq2 + deseq2 + Differential gene expression analysis based on the negative binomial distribution + DESeq2 + DESeq2 + + DESeq2 + R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + Differential gene expression analysis, RNA-Seq analysis + RNA-Seq + To update + https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + Transcriptomics, RNA, Statistics + deseq2 + 2018-11-15 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 + 2.11.40.8 + bioconductor-deseq2 + 1.42.0 + Differential gene expression analysis, RNA-Seq analysis + RNA-Seq + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 97434 + 109474 + 11355 + 12514 + 183905 + 246475 + 24951 + 31957 + 18551 + 20166 + 2647 + 2905 + 299890 + 376115 + 38953 + 47376 + False + + + + deseq2_normalization + deseq2_normalization + Normalizes gene hitlists + + + + + + + + To update + http://artbio.fr + RNA, Transcriptomics, Sequence Analysis, Statistics + deseq2_normalization + 2018-01-05 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization + https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization + 1.40.2+galaxy0 + bioconductor-deseq2 + 1.42.0 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + dexseq + dexseq, dexseq_count, plotdexseq + Inference of differential exon usage in RNA-Seq + dexseq + dexseq + + DEXSeq + The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. + Enrichment analysis, Exonic splicing enhancer prediction + RNA-Seq + Up-to-date + https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html + Transcriptomics, RNA, Statistics + dexseq + 2018-05-02 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq + 1.48.0 + bioconductor-dexseq + 1.48.0 + Enrichment analysis, Exonic splicing enhancer prediction + RNA-Seq + 3 + 3 + 3 + 3 + 3 + 3 + 3 + 3 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 3 + 3 + 0 + 14874 + 16927 + 533 + 837 + 18475 + 28854 + 1403 + 2568 + 3854 + 4271 + 141 + 163 + 37203 + 50052 + 2077 + 3568 + False + + + + dropletutils + dropletutils_empty_drops, dropletutils_read_10x + De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_dropletutils + 2019-01-22 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils + 1.0.4 + dropletutils-scripts + 0.0.5 + + + 2 + 2 + 2 + 0 + 2 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 0 + 0 + 1900 + 1901 + 412 + 413 + 609 + 609 + 131 + 131 + 0 + 0 + 0 + 0 + 2509 + 2510 + 543 + 544 + False + + + + dropletutils + dropletutils + DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data + dropletutils + dropletutils + + DropletUtils + Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. + Loading, Community profiling + Gene expression, RNA-seq, Sequencing, Transcriptomics + To update + https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html + Single Cell, Sequence Analysis + dropletutils + 2019-09-02 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils + 1.10.0 + bioconductor-dropletutils + 1.22.0 + + Sequencing, Transcriptomics + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 4413 + 4442 + 430 + 431 + 4403 + 4403 + 255 + 255 + 1816 + 1816 + 33 + 33 + 10632 + 10661 + 718 + 719 + False + + + + edger + edger + Perform RNA-Seq differential expression analysis using edgeR pipeline + edger + edger + + edgeR + Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + Differential gene expression analysis + Genetics, RNA-Seq, ChIP-seq + To update + http://bioconductor.org/packages/release/bioc/html/edgeR.html + Transcriptomics, RNA, Statistics + edger + 2019-02-08 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger + https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger + 3.36.0 + bioconductor-edger + 4.0.16 + Differential gene expression analysis + Genetics, RNA-Seq, ChIP-seq + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 19294 + 20905 + 2423 + 2618 + 48876 + 58723 + 6341 + 7527 + 8010 + 8705 + 846 + 892 + 76180 + 88333 + 9610 + 11037 + False + + + + egsea + egsea + This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing + egsea + egsea + + EGSEA + This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. + Gene set testing + Systems biology + To update + https://bioconductor.org/packages/release/bioc/html/EGSEA.html + Transcriptomics, RNA, Statistics + egsea + 2018-01-01 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea + 1.20.0 + bioconductor-egsea + 1.28.0 + Gene set testing + Systems biology + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 2809 + 3060 + 371 + 402 + 5179 + 5179 + 759 + 759 + 1931 + 1931 + 226 + 226 + 9919 + 10170 + 1356 + 1387 + False + + + + episcanpy + episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess + EpiScanpy – Epigenomics single cell analysis in python + episcanpy + episcanpy + + epiScanpy + Epigenomics Single Cell Analysis in Python. + Enrichment analysis, Imputation + Epigenomics, Cell biology, DNA + To update + https://github.com/colomemaria/epiScanpy + Single Cell, Epigenetics + episcanpy + 2023-03-22 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy + 0.3.2 + episcanpy + 0.4.0 + Enrichment analysis, Imputation + Epigenomics, Cell biology, DNA + 3 + 3 + 3 + 0 + 3 + 3 + 3 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 0 + 0 + 880 + 880 + 80 + 80 + 221 + 221 + 37 + 37 + 49 + 49 + 3 + 3 + 1150 + 1150 + 120 + 120 + False + + + + fgsea + fgsea + Perform gene set testing using fgsea + fgsea + fgsea + + fgsea + The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. + Gene-set enrichment analysis + Genetics + To update + https://bioconductor.org/packages/release/bioc/html/fgsea.html + Visualization, Transcriptomics, Statistics + fgsea + 2018-10-19 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea + 1.8.0+galaxy1 + bioconductor-fgsea + 1.28.0 + Gene-set enrichment analysis + Genetics + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 5618 + 5820 + 582 + 607 + 21673 + 21673 + 938 + 938 + 869 + 869 + 110 + 110 + 28160 + 28362 + 1630 + 1655 + False + + + + garnett + garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file + De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_garnett + 2020-04-03 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett + 0.2.8 + garnett-cli + 0.0.5 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 27 + 27 + 11 + 11 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 27 + 27 + 11 + 11 + False + + + + gsc_filter_cells + filter_cells + Filter single cell RNAseq data on libray depth and number of detected genes + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_filter_cells + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_filter_genes + filter_genes + Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_filter_genes + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_gene_expression_correlations + single_cell_gene_expression_correlations + Compute single-cell paire-wise gene expressions correlations + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_gene_expression_correlations + 2019-06-24 + artbio + https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_high_dimensions_visualisation + high_dimensions_visualisation + Generates PCA, t-SNE and HCPC visualisation + + + + + + + + To update + http://artbio.fr + Transcriptomics, Visualization + gsc_high_dimensions_visualisation + 2019-07-09 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation + 4.3+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_mannwhitney_de + mannwhitney_de + Perform a mann-whitney differential testing between two sets of gene expression data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_mannwhitney_de + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de + 4.1.3+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_scran_normalize + scran_normalize + Normalize raw counts using scran + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_scran_normalize + 2019-09-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize + 1.28.1+galaxy0 + bioconductor-scran + 1.30.0 + + + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 89 + 89 + 24 + 24 + 3 + 3 + 2 + 2 + 10 + 10 + 2 + 2 + 102 + 102 + 28 + 28 + False + + + + gsc_signature_score + signature_score + Compute signature scores from single cell RNAseq data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_signature_score + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score + 2.3.9+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + heinz + heinz_bum, heinz, heinz_scoring, heinz_visualization + An algorithm for identification of the optimal scoring subnetwork. + heinz + heinz, bionet + + Heinz + Tool for single-species active module discovery. + Pathway or network analysis + Genetics, Gene expression, Molecular interactions, pathways and networks + To update + https://github.com/ls-cwi/heinz + Transcriptomics, Visualization, Statistics + heinz + 2018-06-11 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz + https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz + 1.0 + bioconductor-bionet + 1.62.0 + Pathway or network analysis + Genetics, Gene expression, Molecular interactions, pathways and networks + 4 + 4 + 4 + 0 + 4 + 4 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 4 + 4 + 4 + 0 + 1281 + 1434 + 367 + 442 + 1559 + 1559 + 636 + 636 + 678 + 678 + 52 + 52 + 3518 + 3671 + 1055 + 1130 + False + + + + infercnv + infercnv + Infer Copy Number Variation from Single-Cell RNA-Seq Data + + + + + + + + Up-to-date + https://github.com/broadinstitute/infercnv + Transcriptomics, Variant Analysis + infercnv + 2024-07-23 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv + https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv + 1.20.0 + bioconductor-infercnv + 1.20.0 + + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 10 + 10 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 10 + 10 + 2 + 2 + False + + + + monocle3 + monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers + De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_monocle3 + 2019-09-09 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 + 0.1.4 + monocle3-cli + 0.0.9 + + + 9 + 0 + 9 + 0 + 9 + 0 + 9 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3610 + 3610 + 559 + 559 + 1728 + 1728 + 434 + 434 + 0 + 0 + 0 + 0 + 5338 + 5338 + 993 + 993 + False + + + + multigsea + multigsea + GSEA-based pathway enrichment analysis for multi-omics data + multiGSEA + multiGSEA + + multiGSEA + A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. + Gene-set enrichment analysis, Aggregation, Pathway analysis + Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules + Up-to-date + https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html + Transcriptomics, Proteomics, Statistics + multigsea + 2023-06-07 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea + 1.12.0 + bioconductor-multigsea + 1.12.0 + Gene-set enrichment analysis, Aggregation, Pathway analysis + Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 106 + 106 + 25 + 25 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 106 + 106 + 25 + 25 + False + + + + music_deconvolution + music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution + Multi-subject Single Cell deconvolution (MuSiC) + + + + + + + + Up-to-date + https://github.com/xuranw/MuSiC + Transcriptomics + music + 2021-09-12 + bgruening + https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ + https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution + 0.1.1 + music-deconvolution + 0.1.1 + + + 5 + 5 + 4 + 0 + 5 + 5 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 5 + 0 + 0 + 2801 + 2801 + 289 + 289 + 364 + 364 + 80 + 80 + 1357 + 1357 + 21 + 21 + 4522 + 4522 + 390 + 390 + False + + + + pyscenic + pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn + PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ + + + + + + + + To update + + Transcriptomics, RNA, Sequence Analysis + suite_pyscenic + 2024-08-20 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic + 0.12.1 + + + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + raceid + raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory + RaceID3, StemID2, FateID - scRNA analysis + + + + + + + + To update + https://github.com/dgrun/RaceID3_StemID2_package/ + Single Cell, Transcriptomics + + 2021-04-14 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid + 0.2.3 + r-raceid + 0.1.3 + + + 5 + 5 5 - 5 - 5 1 5 5 @@ -687,7 +2899,244 @@ 9414 1507 1630 + False + + + + rgrnastar + rna_star, rna_starsolo + RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper + star + star + + STAR + Ultrafast universal RNA-seq data aligner + Sequence alignment + RNA-Seq, Transcriptomics + To update + https://github.com/alexdobin/STAR + Next Gen Mappers, Transcriptomics + rgrnastar + 2023-02-27 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar + https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar + 2.7.11a + star + 2.7.11b + Sequence alignment + RNA-Seq, Transcriptomics + 2 + 2 + 2 + 2 + 2 + 2 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 0 + 2 + 0 + 0 + 0 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 2 + 2 + 0 + 438078 + 473957 + 10142 + 10900 + 325474 + 403925 + 15284 + 18791 + 49662 + 53138 + 1359 + 1449 + 813214 + 931020 + 26785 + 31140 + False + + + + salmon + alevin, salmon, salmonquantmerge + Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. + salmon + salmon + + Salmon + A tool for transcript expression quantification from RNA-seq data + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis + RNA-Seq, Gene expression, Transcriptomics + To update + https://github.com/COMBINE-lab/salmon + Sequence Analysis, RNA, Transcriptomics + + 2019-09-18 + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + 1.10.1 + salmon + 1.10.3 + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis + RNA-Seq, Transcriptomics + 2 + 2 + 3 + 1 + 2 + 2 + 3 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 3 + 3 + 0 + 73085 + 77081 + 2243 + 2319 + 90634 + 122835 + 3402 + 4726 + 13371 + 15818 + 513 + 586 + 177090 + 215734 + 6158 + 7631 + False + + + + sc3 + sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare + De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_sc3 + 2018-11-05 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 + 1.8.0 + sc3-scripts + 0.0.6 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 13 + 13 + 10 + 10 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 13 + 13 + 10 + 10 + False @@ -718,8 +3167,166 @@ 6 6 0 - 6 - 6 + 6 + 6 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 6 + 6 + 6 + 0 + 63789 + 64034 + 2543 + 2547 + 29962 + 29962 + 1185 + 1185 + 18028 + 18028 + 379 + 379 + 111779 + 112024 + 4107 + 4111 + False + + + + scanpy + anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data + scanpy-scripts, command-line wrapper scripts around Scanpy. + + + + + + + + To update + https://scanpy.readthedocs.io + Transcriptomics, Sequence Analysis, RNA + scanpy_scripts + 2020-09-29 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy + 1.9.3 + scanpy-scripts + 1.9.301 + + + 27 + 27 + 27 + 0 + 27 + 27 + 27 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 14 + 13 + 0 + 45501 + 45666 + 4832 + 4868 + 7304 + 7304 + 1846 + 1846 + 3106 + 3106 + 457 + 457 + 55911 + 56076 + 7135 + 7171 + False + + + + scater + scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results + De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scater + 2018-10-11 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater + 1.10.0 + scater-scripts + 0.0.5 + + + 1 + 2 + 6 + 0 + 1 + 2 6 0 0 @@ -746,27 +3353,27 @@ 0 0 0 - 6 - 6 - 6 + 2 + 2 + 2 0 - 63789 - 64034 - 2543 - 2547 - 29962 - 29962 - 1185 - 1185 - 18028 - 18028 - 379 - 379 - 111779 - 112024 - 4107 - 4111 - + 381 + 388 + 99 + 100 + 0 + 0 + 0 + 0 + 297 + 297 + 9 + 9 + 678 + 685 + 108 + 109 + False @@ -845,7 +3452,165 @@ 2274 379 380 + False + + + + sccaf + run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out + SCCAF: Single Cell Clustering Assessment Framework. + + + + + + + + To update + https://github.com/sccaf/sccaf + Transcriptomics + SCCAF + 2019-10-20 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf + 0.0.9 + sccaf + 0.0.10 + + + 4 + 3 + 4 + 0 + 4 + 3 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 110 + 110 + 19 + 19 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 110 + 110 + 19 + 19 + False + + + + sceasy + sceasy_convert + Convert scRNA data object between popular formats + + + + + + + + To update + + Transcriptomics + sceasy + 2019-10-14 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy + 0.0.5 + r-sceasy + 0.0.7 + + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1059 + 1059 + 222 + 222 + 426 + 426 + 71 + 71 + 1 + 1 + 1 + 1 + 1486 + 1486 + 294 + 294 + False @@ -924,7 +3689,7 @@ 1486 294 294 - + False @@ -955,9 +3720,91 @@ 16 16 0 - 16 - 16 - 16 + 16 + 16 + 16 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 16 + 16 + 16 + 0 + 809 + 809 + 78 + 78 + 3 + 3 + 2 + 2 + 105 + 105 + 16 + 16 + 917 + 917 + 96 + 96 + False + + + + scmap + scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features + De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scmap + 2019-08-30 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap + 1.6.4 + scmap-cli + 0.1.0 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 0 0 0 @@ -981,29 +3828,26 @@ 0 0 0 + 1 0 0 - 16 - 16 - 16 + 97 + 97 + 41 + 41 0 - 809 - 809 - 78 - 78 - 3 - 3 - 2 - 2 - 105 - 105 - 16 - 16 - 917 - 917 - 96 - 96 - + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 97 + 97 + 41 + 41 + False @@ -1082,7 +3926,165 @@ 1419 96 100 + False + + + + scpred + scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model + De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scpred + 2020-04-07 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred + 1.0.2 + scpred-cli + 0.1.0 + + + 0 + 0 + 4 + 0 + 0 + 0 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 25 + 25 + 5 + 5 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 25 + 25 + 5 + 5 + False + + + + seurat + seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features + De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 + + + + + + + + To update + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_seurat + 2018-07-09 + ebi-gxa + + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat + 4.0.0 + seurat-scripts + 4.4.0 + + 14 + 14 + 14 + 11 + 14 + 14 + 14 + 11 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 19 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2296 + 2328 + 673 + 676 + 141 + 141 + 39 + 39 + 0 + 0 + 0 + 0 + 2437 + 2469 + 712 + 715 + False @@ -1161,7 +4163,7 @@ 153 16 16 - + False @@ -1240,7 +4242,7 @@ 463 110 110 - + False @@ -1319,7 +4321,7 @@ 1957 20 20 - + False @@ -1398,7 +4400,86 @@ 0 0 0 + False + + + + ucsc-cell-browser + ucsc_cell_browser + Python pipeline and Javascript scatter plot library for single-cell datasets + + + + + + + + To update + https://cells.ucsc.edu/ + Transcriptomics + ucsc_cell_browser + 2018-09-11 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser + 1.0.0+galaxy1 + ucsc-cell-browser + 1.2.8 + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 0 + 965 + 975 + 178 + 181 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 965 + 975 + 178 + 181 + False @@ -1477,7 +4558,7 @@ 89568 2183 2316 - + False @@ -1556,7 +4637,86 @@ 45 11 11 + False + + + + volcanoplot + volcanoplot + Tool to create a Volcano Plot + + + + + + + To update + https://ggplot2.tidyverse.org/ + Visualization, Transcriptomics, Statistics + volcanoplot + 2018-10-14 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot + https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot + 0.0.6 + r-ggplot2 + 2.2.1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 34917 + 36852 + 3670 + 3786 + 54931 + 54931 + 5597 + 5597 + 7183 + 7183 + 905 + 905 + 97031 + 98966 + 10172 + 10288 + False diff --git a/communities/spoc/resources/tools.tsv b/communities/spoc/resources/tools.tsv index cdd045ef..c0645bef 100644 --- a/communities/spoc/resources/tools.tsv +++ b/communities/spoc/resources/tools.tsv @@ -1,19 +1,59 @@ Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True +cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True +deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True +dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True +dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True +edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True +egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True +fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True +infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True +music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True +pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True +scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True +seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True +spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True +volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True diff --git a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv index cdd045ef..0564adfb 100644 --- a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv +++ b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv @@ -1,19 +1,106 @@ Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 True False False +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True +arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 True False False +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 True False False +brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 True False False +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 True False False +chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 True False False +cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 True False False +cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True +cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 True False False +cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 True False False +cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 True False False +cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 True False False +cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 True False False +cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 True False False +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True +deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True +dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True +dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True +edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True +egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True False False +fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True +genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 True False False +gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 True False False +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True +infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True +isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 True False False +kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 True False False +limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True False False +masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 True False False +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 True False False +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True +music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 True False False +pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 True False False +psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 True False False +pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True False False +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True +repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 True False False +repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 True False False +rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 True False False +rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True False False +ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 True False False +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True +scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True +seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True +slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 True False False +sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 True False False +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True +spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 True False False +stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 True False False +tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 True False False +transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 True False False +trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 True False False +trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 True False False +tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 True False False +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True +volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True diff --git a/communities/spoc/resources/tools_wordcloud.png b/communities/spoc/resources/tools_wordcloud.png index 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z?B8K_4vR&ED5V9D0ea1&{P6e(Yn0!Bv({3@UXkzGbEJ7;eyCGUpRG8t)Di#H;I~yc z|AnG$9&*|F*=9+o3HDuJJ_#J<33-;epRJsJdgbvjTemlB4PIb|2OtJsBVk4 X7L=7tPNb${|M^5p@loyr!&m Date: Mon, 4 Nov 2024 17:34:38 +0100 Subject: [PATCH 4/9] Add Marisa seuratv5 tools --- .../spoc/lab/tool_panel/hca-seurat.yml | 28 ++++++ .../spoc/lab/tool_panel/hca-seurat.yml.lock | 83 ++++++++++++++++ communities/spoc/lab/tool_panel/seurat.yml | 40 +++----- .../spoc/lab/tool_panel/seurat.yml.lock | 96 +++++++------------ .../spoc/lab/tool_panel/tool_panel_view.yml | 68 ++++++------- 5 files changed, 191 insertions(+), 124 deletions(-) create mode 100644 communities/spoc/lab/tool_panel/hca-seurat.yml create mode 100644 communities/spoc/lab/tool_panel/hca-seurat.yml.lock diff --git a/communities/spoc/lab/tool_panel/hca-seurat.yml b/communities/spoc/lab/tool_panel/hca-seurat.yml new file mode 100644 index 00000000..df7bdd20 --- /dev/null +++ b/communities/spoc/lab/tool_panel/hca-seurat.yml @@ -0,0 +1,28 @@ +tool_panel_section_label: HCA-Seurat +tools: +- name: seurat_create_seurat_object + owner: ebi-gxa +- name: seurat_export_cellbrowser + owner: ebi-gxa +- name: seurat_filter_cells + owner: ebi-gxa +- name: seurat_find_clusters + owner: ebi-gxa +- name: seurat_find_markers + owner: ebi-gxa +- name: seurat_find_neighbours + owner: ebi-gxa +- name: seurat_find_variable_genes + owner: ebi-gxa +- name: seurat_normalise_data + owner: ebi-gxa +- name: seurat_dim_plot + owner: ebi-gxa +- name: seurat_read10x + owner: ebi-gxa +- name: seurat_run_pca + owner: ebi-gxa +- name: seurat_run_tsne + owner: ebi-gxa +- name: seurat_scale_data + owner: ebi-gxa diff --git a/communities/spoc/lab/tool_panel/hca-seurat.yml.lock b/communities/spoc/lab/tool_panel/hca-seurat.yml.lock new file mode 100644 index 00000000..e311102e --- /dev/null +++ b/communities/spoc/lab/tool_panel/hca-seurat.yml.lock @@ -0,0 +1,83 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: HCA-Seurat +tools: +- name: seurat_create_seurat_object + owner: ebi-gxa + revisions: + - f8865ae30723 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_export_cellbrowser + owner: ebi-gxa + revisions: + - 36221da750e8 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_filter_cells + owner: ebi-gxa + revisions: + - cd9f564bd63f + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_clusters + owner: ebi-gxa + revisions: + - d541e9e62beb + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_markers + owner: ebi-gxa + revisions: + - 07fc9f4841b3 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_neighbours + owner: ebi-gxa + revisions: + - ba897c57bdd9 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_variable_genes + owner: ebi-gxa + revisions: + - 948fc0276b4f + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_normalise_data + owner: ebi-gxa + revisions: + - 3f49bc9c9213 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_dim_plot + owner: ebi-gxa + revisions: + - 64174ac50d78 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_read10x + owner: ebi-gxa + revisions: + - f5db0e853f57 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_pca + owner: ebi-gxa + revisions: + - 8ded486b0014 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_tsne + owner: ebi-gxa + revisions: + - 0db997e4a81d + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_scale_data + owner: ebi-gxa + revisions: + - 5e9ba303f9e1 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat diff --git a/communities/spoc/lab/tool_panel/seurat.yml b/communities/spoc/lab/tool_panel/seurat.yml index 0b95e939..d797e131 100644 --- a/communities/spoc/lab/tool_panel/seurat.yml +++ b/communities/spoc/lab/tool_panel/seurat.yml @@ -1,28 +1,16 @@ tool_panel_section_label: Seurat tools: -- name: seurat_create_seurat_object - owner: ebi-gxa -- name: seurat_export_cellbrowser - owner: ebi-gxa -- name: seurat_filter_cells - owner: ebi-gxa -- name: seurat_find_clusters - owner: ebi-gxa -- name: seurat_find_markers - owner: ebi-gxa -- name: seurat_find_neighbours - owner: ebi-gxa -- name: seurat_find_variable_genes - owner: ebi-gxa -- name: seurat_normalise_data - owner: ebi-gxa -- name: seurat_dim_plot - owner: ebi-gxa -- name: seurat_read10x - owner: ebi-gxa -- name: seurat_run_pca - owner: ebi-gxa -- name: seurat_run_tsne - owner: ebi-gxa -- name: seurat_scale_data - owner: ebi-gxa +- name: create_seurat + owner: iuc +- name: inspect_and_manipulate + owner: iuc +- name: integrate + owner: iuc +- name: normalize_select_features_scale + owner: iuc +- name: reduce_dimensions + owner: iuc +- name: neighbors_clusters_markers + owner: iuc +- name: plot + owner: iuc diff --git a/communities/spoc/lab/tool_panel/seurat.yml.lock b/communities/spoc/lab/tool_panel/seurat.yml.lock index cf910f55..d7e9d57b 100644 --- a/communities/spoc/lab/tool_panel/seurat.yml.lock +++ b/communities/spoc/lab/tool_panel/seurat.yml.lock @@ -3,81 +3,49 @@ install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Seurat tools: -- name: seurat_create_seurat_object - owner: ebi-gxa +- name: create_seurat + owner: iuc revisions: - - f8865ae30723 - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_export_cellbrowser - owner: ebi-gxa +- name: inspect_and_manipulate + owner: iuc revisions: - - 36221da750e8 - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_filter_cells - owner: ebi-gxa +- name: integrate + owner: iuc revisions: - - cd9f564bd63f - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_find_clusters - owner: ebi-gxa +- name: neighbors_clusters_markers + owner: iuc revisions: - - d541e9e62beb - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_find_markers - owner: ebi-gxa +- name: normalize_select_features_scale + owner: iuc revisions: - - 07fc9f4841b3 - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_find_neighbours - owner: ebi-gxa +- name: plot + owner: iuc revisions: - - ba897c57bdd9 - tool_panel_section_id: seurat + - + tool_panel_section_id: Seurat tool_panel_section_label: Seurat -- name: seurat_find_variable_genes - owner: ebi-gxa +- name: reduce_dimensions + owner: iuc revisions: - - 948fc0276b4f - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_normalise_data - owner: ebi-gxa - revisions: - - 3f49bc9c9213 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_dim_plot - owner: ebi-gxa - revisions: - - 64174ac50d78 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_read10x - owner: ebi-gxa - revisions: - - f5db0e853f57 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_run_pca - owner: ebi-gxa - revisions: - - 8ded486b0014 - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_run_tsne - owner: ebi-gxa - revisions: - - 0db997e4a81d - tool_panel_section_id: seurat - tool_panel_section_label: Seurat -- name: seurat_scale_data - owner: ebi-gxa - revisions: - - 5e9ba303f9e1 - tool_panel_section_id: seurat + - 0cb889db0910 + - 32c5c85cbc12 + - c0b037b12765 + - c5ac926c838f + - e1c3c2f2a834 + tool_panel_section_id: Seurat tool_panel_section_label: Seurat diff --git a/communities/spoc/lab/tool_panel/tool_panel_view.yml b/communities/spoc/lab/tool_panel/tool_panel_view.yml index 126685fd..08bdfec1 100644 --- a/communities/spoc/lab/tool_panel/tool_panel_view.yml +++ b/communities/spoc/lab/tool_panel/tool_panel_view.yml @@ -109,38 +109,6 @@ items: id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim - type: tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers -- id: seurat - type: section - name: Seurat - items: - - type: tool - id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_create_seurat_object/seurat_create_seurat_object - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne - - type: tool - id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data - id: inference type: section name: Inference @@ -186,7 +154,7 @@ items: - id: hca-scanpy type: section name: HCA-Scanpy - items: + items: - type: tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops - type: tool @@ -245,10 +213,42 @@ items: id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_multiplet_scrublet/scanpy_multiplet_scrublet - type: tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap +- id: seurat + type: section + name: Seurat + items: + - type: tool + id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_create_seurat_object/seurat_create_seurat_object + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne + - type: tool + id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data - id: raceid type: section name: RaceID - items: + items: - type: tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters - type: tool From 458d7386401920b019df69cf724012871230973b Mon Sep 17 00:00:00 2001 From: paulzierep Date: Tue, 5 Nov 2024 12:11:08 +0100 Subject: [PATCH 5/9] update CI, only run on internal PR and Dev push --- .github/workflows/run_tests.yaml | 62 +++++++++++++++++++++++++++++--- sources/README.md | 9 +++++ 2 files changed, 67 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 5ca93a36..38d40e0a 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -1,9 +1,47 @@ name: Run tests -on: [push, pull_request] + +# This GitHub Actions workflow is designed to automate testing for the project. +# It triggers under two conditions: +# 1. Pull requests targeting the main branch, ensuring that internal changes +# are validated before merging. +# 2. Pushes to the dev branch, allowing for continuous integration +# as changes are made directly to the development branch. +# +# The workflow consists of three main jobs: +# - **test-tools**: Runs tests for tools extracted from the repository. +# - **test-tutorials**: Runs tests for community tutorials. +# - **test-workflows**: Runs tests for workflow scripts. +# +# Each job includes the following steps: +# - Checkout the repository code. +# - Set up the Python environment using the specified version. +# - Install required dependencies. +# - Execute scripts for extraction and filtering of tools, tutorials, or workflows. +# +# This ensures that the code remains reliable and functional as new changes are introduced. + +on: + pull_request: + branches: + - main # Trigger on pull requests targeting the main branch + push: + branches: + - dev # Trigger on pushes to the dev branch jobs: test-tools: runs-on: ubuntu-20.04 + # This job runs tests for tools. + # It checks for internal pull requests targeting the main branch, + # as well as pushes to the dev branch. + # The workflow performs the following steps: + # 1. Checkout the repository code. + # 2. Set up Python environment using the specified version. + # 3. Install required Python packages. + # 4. Extract tools using a provided script. + # 5. Filter community tools using a provided script. + # 6. Format tools into an interactive table and generate a word cloud. + if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' strategy: matrix: python-version: ['3.11'] @@ -14,7 +52,7 @@ jobs: - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install requirement + - name: Install requirements run: python -m pip install -r requirements.txt - name: Tool extraction run: | @@ -27,8 +65,19 @@ jobs: - name: Create interactive table and wordcloud run: | bash sources/bin/format_tools.sh + test-tutorials: runs-on: ubuntu-20.04 + # This job runs tests for tutorials. + # Similar to the tools job, it checks for internal pull requests + # to the main branch and pushes to the dev branch. + # The workflow performs the following steps: + # 1. Checkout the repository code. + # 2. Set up Python environment using the specified version. + # 3. Install required Python packages. + # 4. Extract tutorials using a provided script. + # 5. Filter community tutorials using a provided script. + if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' strategy: matrix: python-version: ['3.11'] @@ -38,7 +87,7 @@ jobs: - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install requirement + - name: Install requirements run: python -m pip install -r requirements.txt - name: Tutorial extraction run: | @@ -48,8 +97,13 @@ jobs: - name: Tutorial filtering run: | bash sources/bin/get_community_tutorials.sh test + test-workflows: runs-on: ubuntu-20.04 + # This job runs tests for workflows. + # It performs the same checks as the other jobs, ensuring + # quality for workflow scripts. + if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' strategy: matrix: python-version: ['3.11'] @@ -59,7 +113,7 @@ jobs: - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install requirement + - name: Install requirements run: python -m pip install -r requirements.txt - name: Workflow extraction run: | diff --git a/sources/README.md b/sources/README.md index 6d353ea7..2cb84a39 100644 --- a/sources/README.md +++ b/sources/README.md @@ -202,6 +202,15 @@ $ python sources/bin/create_interactive_table.py \ ## Development +### Contributing + +To contribute to the CoDex Source code fork the repository, create a branch and add your changes. Then make a +pull request to the **dev branch** of the CoDex repository. Upon review the maintainer will merge your pull request. +Automatic tests will run on the dev branch. +When the tests succeed a maintainer will merge the dev branch into main. Feel free to ping the maintainers to speed up the process. +The reason we are not running the tests directly on the pull request branch is, that this does not allow to access the +GitHub secrets, that are required to run the tests. + ### Tools To make a test run of the tool to check its functionalities follow [Usage](#Usage) to set-up the environnement and the API key, then run From d59f82d1427ffeaa6de6e6dd1982a0e9b1af8427 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Tue, 5 Nov 2024 17:22:46 +0100 Subject: [PATCH 6/9] Update sources/README.md --- sources/README.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/sources/README.md b/sources/README.md index 2cb84a39..53b7bd16 100644 --- a/sources/README.md +++ b/sources/README.md @@ -204,12 +204,17 @@ $ python sources/bin/create_interactive_table.py \ ### Contributing -To contribute to the CoDex Source code fork the repository, create a branch and add your changes. Then make a -pull request to the **dev branch** of the CoDex repository. Upon review the maintainer will merge your pull request. +To contribute to the CoDex Source code: +1. fork the repository, +2. create a branch and add your changes +3. make a pull request to the **dev branch** of the CoDex repository. + +Upon review the maintainer will merge your pull request. Automatic tests will run on the dev branch. + When the tests succeed a maintainer will merge the dev branch into main. Feel free to ping the maintainers to speed up the process. -The reason we are not running the tests directly on the pull request branch is, that this does not allow to access the -GitHub secrets, that are required to run the tests. + +The reason we are not running the tests directly on the pull request branch is, that this does not allow to access the GitHub secrets, that are required to run the tests. ### Tools From 68df393e81648c1b1568f2ba9bc5c12674524de2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 6 Nov 2024 14:18:07 +0100 Subject: [PATCH 7/9] Split existing tool filtering command into 2 commands generating community reviewable TSV (#212) * Split filter command into 2 commands generating community reviewable TSV * Update community resources * Add test conditional for format script --- .github/workflows/run_tests.yaml | 2 +- communities/all/resources/tools.tsv | 1476 - communities/assembly/resources/tools.tsv | 178 - .../tools_filtered_by_ts_categories.json | 16013 ++ .../tools_filtered_by_ts_categories.tsv | 356 +- .../biodiversity/metadata/tool_status.tsv | 0 communities/biodiversity/resources/tools.tsv | 134 - .../tools_filtered_by_ts_categories.json | 11975 ++ .../tools_filtered_by_ts_categories.tsv | 266 +- communities/genome/resources/tools.tsv | 1476 - .../tools_filtered_by_ts_categories.json | 132946 +++++++++++++++ .../tools_filtered_by_ts_categories.tsv | 2950 +- communities/imaging/metadata/tool_status.tsv | 0 communities/imaging/resources/tools.tsv | 68 - .../tools_filtered_by_ts_categories.json | 6186 + .../tools_filtered_by_ts_categories.tsv | 136 +- .../machine-learning/metadata/tool_status.tsv | 1 + .../machine-learning/resources/tools.tsv | 13 - .../tools_filtered_by_ts_categories.json | 1087 + .../tools_filtered_by_ts_categories.tsv | 26 +- communities/metabolomics/resources/tools.tsv | 183 - .../tools_filtered_by_ts_categories.json | 16440 ++ .../tools_filtered_by_ts_categories.tsv | 366 +- .../microgalaxy/metadata/tool_status.tsv | 1 + .../{tools.tsv => curated_tools.tsv} | 578 +- .../resources/curated_tools_w_biotools.tsv | 219 + .../resources/curated_tools_wo_biotools.tsv | 71 + .../tools_filtered_by_ts_categories.json | 76549 +++++++++ .../tools_filtered_by_ts_categories.tsv | 1662 +- .../microgalaxy/resources/tools_wordcloud.png | Bin 323992 -> 324880 bytes .../microgalaxy/resources/workflows.html | 2799 + .../microgalaxy/resources/workflows.tsv | 144 + communities/proteomics/resources/tools.tsv | 1476 - .../tools_filtered_by_ts_categories.json | 8536 + .../tools_filtered_by_ts_categories.tsv | 1571 +- communities/spoc/metadata/tool_status.tsv | 1 + .../{tools.tsv => curated_tools.tsv} | 118 +- .../resources/curated_tools_w_biotools.tsv | 19 + .../resources/curated_tools_wo_biotools.tsv | 41 + .../tools_filtered_by_ts_categories.json | 9742 ++ .../tools_filtered_by_ts_categories.tsv | 212 +- .../spoc/resources/tools_wordcloud.png | Bin 151440 -> 151440 bytes sources/bin/extract_galaxy_tools.py | 176 +- sources/bin/format_tools.sh | 34 +- sources/bin/get_community_tools.sh | 78 +- 45 files changed, 286407 insertions(+), 9898 deletions(-) delete mode 100644 communities/all/resources/tools.tsv delete mode 100644 communities/assembly/resources/tools.tsv create mode 100644 communities/assembly/resources/tools_filtered_by_ts_categories.json delete mode 100644 communities/biodiversity/metadata/tool_status.tsv delete mode 100644 communities/biodiversity/resources/tools.tsv create mode 100644 communities/biodiversity/resources/tools_filtered_by_ts_categories.json delete mode 100644 communities/genome/resources/tools.tsv create mode 100644 communities/genome/resources/tools_filtered_by_ts_categories.json delete mode 100644 communities/imaging/metadata/tool_status.tsv delete mode 100644 communities/imaging/resources/tools.tsv create mode 100644 communities/imaging/resources/tools_filtered_by_ts_categories.json delete mode 100644 communities/machine-learning/resources/tools.tsv create mode 100644 communities/machine-learning/resources/tools_filtered_by_ts_categories.json delete mode 100644 communities/metabolomics/resources/tools.tsv create mode 100644 communities/metabolomics/resources/tools_filtered_by_ts_categories.json rename communities/microgalaxy/resources/{tools.tsv => curated_tools.tsv} (95%) create mode 100644 communities/microgalaxy/resources/curated_tools_w_biotools.tsv create mode 100644 communities/microgalaxy/resources/curated_tools_wo_biotools.tsv create mode 100644 communities/microgalaxy/resources/tools_filtered_by_ts_categories.json create mode 100644 communities/microgalaxy/resources/workflows.html create mode 100644 communities/microgalaxy/resources/workflows.tsv delete mode 100644 communities/proteomics/resources/tools.tsv create mode 100644 communities/proteomics/resources/tools_filtered_by_ts_categories.json rename communities/spoc/resources/{tools.tsv => curated_tools.tsv} (94%) create mode 100644 communities/spoc/resources/curated_tools_w_biotools.tsv create mode 100644 communities/spoc/resources/curated_tools_wo_biotools.tsv create mode 100644 communities/spoc/resources/tools_filtered_by_ts_categories.json diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 38d40e0a..012bea3b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -64,7 +64,7 @@ jobs: bash sources/bin/get_community_tools.sh test - name: Create interactive table and wordcloud run: | - bash sources/bin/format_tools.sh + bash sources/bin/format_tools.sh test test-tutorials: runs-on: ubuntu-20.04 diff --git a/communities/all/resources/tools.tsv b/communities/all/resources/tools.tsv deleted file mode 100644 index 18a72c7c..00000000 --- a/communities/all/resources/tools.tsv +++ /dev/null @@ -1,1476 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source 2015-11-17 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 474 2914 132 163 0 0 0 0 0 0 0 0 474 2914 132 163 -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services 2020-06-29 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 3600 3760 883 911 6 6 4 4 0 0 0 0 3606 3766 887 915 -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services 2017-08-11 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source 2022-03-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers batched_lastz 2024-04-30 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 5 5 0 0 0 0 123 123 5 5 -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter 2019-03-15 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services 2018-11-05 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired 2019-12-16 nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk 2019-08-27 nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster 2016-01-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko 2018-04-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services 2023-04-07 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.16 genoboo 0.4.16 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali 2020-03-30 nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation 2018-04-24 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 377 400 17 17 0 0 0 0 0 0 0 0 377 400 17 17 -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 -jbrowse jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container 2016-11-08 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers kegalign 2024-08-29 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 0.1.2.7 kegalign-full 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 5 5 1 1 -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco 2018-06-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko 2018-04-12 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat 2020-03-24 nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names 2017-05-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 514 573 69 83 0 0 0 0 0 0 0 0 514 573 69 83 -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps 2016-01-29 earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign 2024-04-18 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.7 segalign-galaxy 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 252 252 47 47 0 0 0 0 252 252 47 47 -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler 2019-04-15 nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services 2018-06-20 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -unzip unzip Unzip file To update https://github.com/bmcv Convert Formats unzip 2019-08-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 6.0 unzip 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6942 7024 1345 1356 1 1 1 1 2461 2461 266 266 9404 9486 1612 1623 -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 -10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq 2022-05-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 307 307 80 80 8 8 3 3 3 3 1 1 318 318 84 84 -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 -add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file 2020-11-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 15933 15933 378 378 1736 1736 214 214 380 380 28 28 18049 18049 620 620 -add_value addValue Add a value as a new column. To update Text Manipulation add_value 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 37860 374587 1293 1610 17588 293713 1243 6197 3873 4397 202 229 59321 672697 2738 8036 -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 226 308 27 35 2615 45557 302 2284 482 522 32 36 3323 46387 361 2355 -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 -bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph 2015-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 -bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 24164 25149 1320 1480 17537 203397 1330 17491 15654 15992 291 351 57355 244538 2941 19322 -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 -canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu 2018-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 De-novo assembly Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13360 14618 1383 1444 0 0 0 0 3542 3542 385 385 16902 18160 1768 1829 -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 -ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 175 28 39 0 0 0 0 0 0 0 0 88 175 28 39 -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 -change_case ChangeCase Convert column case. To update Text Manipulation change_case 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 10606 12531 2204 2547 9044 17167 1748 2394 923 938 240 245 20573 30636 4192 5186 -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 -cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 513 813 18 35 2406 30579 156 1547 1353 1393 17 20 4272 32785 191 1602 -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 -column_arrange_by_header bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header 2015-03-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5356 5636 446 484 2026 2026 375 375 1400 1531 117 138 8782 9193 938 997 -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 -complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 187 233 15 20 495 4810 165 836 405 451 7 7 1087 5494 187 863 -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 -concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 575128 575441 694 783 43420 85345 629 3508 19330 19418 104 117 637878 680204 1427 4408 -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2173 28 368 195 205 8 8 242 2378 36 376 -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 23589 28986 1061 1200 23507 160693 2302 8699 5413 6446 251 329 52509 196125 3614 10228 -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1560 1725 43 58 4328 44209 193 2113 283 316 16 18 6171 46250 252 2189 -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 -cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular 2014-12-22 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 1208 43 97 1334 2683 101 479 0 0 0 0 2222 3891 144 576 -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1973168 2034965 11939 12833 352364 803522 12967 30199 128777 133584 2341 2572 2454309 2972071 27247 45604 -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 -dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator 2013-11-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 69 26 30 0 304 0 133 0 0 0 0 59 373 26 163 -diff diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff 2020-03-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 362 362 99 99 23 23 17 17 0 0 0 0 385 385 116 116 -diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 -edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta 2022-10-16 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4495 4495 111 111 0 0 0 0 0 0 0 0 4495 4495 111 111 -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg 2018-03-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 160 252 17 21 0 0 0 0 0 0 0 0 160 252 17 21 -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6690 8818 554 612 0 0 0 0 0 0 0 0 6690 8818 554 612 -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 -find_subsequences bg_find_subsequences To update find_subsequences 2015-03-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 784 69 79 2820 3047 323 361 20 20 1 1 3394 3851 393 441 -flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 589 731 51 63 2445 32847 304 2549 1214 1294 15 22 4248 34872 370 2634 -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 -footprint footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint 2017-04-18 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 5 5 0 0 0 0 0 0 0 0 57 57 5 5 -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 -get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3768 325011 1462 2044 9350 242043 2201 6583 787 1070 119 146 13905 568124 3782 8773 -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 2018-07-22 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 -hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk 2024-02-03 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 1.0.0 hictk 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 9 9 0 0 0 0 0 0 0 0 17 17 9 9 -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup 2017-03-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 7 0 7 0 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 901 1020 160 184 440 440 111 111 0 0 0 0 1341 1460 271 295 -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 -intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20472 349984 2351 3007 45587 778988 4359 14116 6087 7417 484 561 72146 1136389 7194 17684 -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 -join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15624 330820 1864 2438 52317 513688 10198 39421 1329 1645 213 289 69270 846153 12275 42148 -join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy 2017-11-26 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1980 2697 345 410 0 0 0 0 1081 1081 44 44 3061 3778 389 454 -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 3 4 0 0 0 0 8 10 5 5 15 19 8 9 -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer 2023-12-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 0 0 0 0 0 0 0 0 8 8 2 2 -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 -megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 743 816 103 141 292 2868 82 459 0 0 0 0 1035 3684 185 600 -merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 565922 566630 418 441 45844 107523 671 4353 19828 19994 100 137 631594 694147 1189 4931 -merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 20905 31051 1906 2128 21780 132833 885 3172 1524 1925 122 152 44209 165809 2913 5452 -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit 2016-12-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 -mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 8 8 17 63 6 19 0 0 0 0 26 74 14 27 -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 -mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 49 5 5 81 417 23 118 0 0 0 0 125 466 28 123 -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish 2018-06-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 9284 9694 215 229 0 0 0 0 2358 2358 49 49 11642 12052 264 278 -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 -netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr 2022-08-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 6 6 0 0 0 0 0 0 0 0 12 12 6 6 -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools 2017-09-28 bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat 2022-01-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 109 109 29 29 250 250 84 84 0 0 0 0 359 359 113 113 -pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval 2015-03-06 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 613 640 48 54 1381 7804 201 1552 756 815 22 30 2750 9259 271 1636 -pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3639 3774 414 461 9754 52522 1247 4531 1893 2433 191 318 15286 58729 1852 5310 -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 148572 169964 3525 3682 36694 113826 3910 8163 9713 10577 1475 1598 194979 294367 8910 13443 -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file 2017-02-24 bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 577184 577312 463 492 43900 44233 283 373 2190 2190 112 112 623274 623735 858 977 -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 -sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1155 1251 57 63 2264 18187 189 1748 525 590 10 17 3944 20028 256 1828 -sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python 1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 278 12 26 3554 76029 450 6346 229 345 16 29 3879 76652 478 6401 -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! Up-to-date https://github.com/biod/sambamba SAM sambamba 2016-06-23 bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 1.0.1 sambamba 1.0.1 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 297 297 51 51 0 0 0 0 0 0 0 0 297 297 51 51 -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 281 2284 10 53 0 0 0 0 0 0 0 0 281 2284 10 53 -segemehl segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1095 1306 98 113 0 0 0 0 0 0 0 0 1095 1306 98 113 -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 27232 36366 2184 2789 16648 84460 4191 18767 2785 3276 373 452 46665 124102 6748 22008 -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1620 2660 378 589 10551 24579 682 1851 284 398 67 83 12455 27637 1127 2523 -sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 276 379 30 42 972 9053 146 1008 644 689 5 7 1892 10121 181 1057 -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 -split_file_on_column tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5995 6261 408 453 2150 2150 311 311 26 26 2 2 8171 8437 721 766 -split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection 2019-08-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16415 16623 968 984 9133 9133 672 672 4140 4140 148 148 29688 29896 1788 1804 -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 -splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta 2015-10-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1772 1811 278 294 3012 3012 564 564 0 0 0 0 4784 4823 842 858 -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 -stress_ng stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng 2021-03-04 bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 3 3 0 0 0 0 0 0 0 0 62 62 3 3 -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 -subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 566512 567199 410 470 49985 184650 1473 7631 20648 20897 155 188 637145 772746 2038 8289 -subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1178 1450 124 141 3169 40539 636 3435 799 950 26 38 5146 42939 786 3614 -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar 2013-12-02 devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16526 64515 2803 7456 0 0 0 0 16526 64515 2803 7456 -tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2188 2220 33 38 0 0 0 0 0 0 0 0 2188 2220 33 38 -tabular_to_fasta tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 329032 333057 1489 1702 79033 215770 2441 8587 27876 33727 296 360 435941 582554 4226 10649 -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 -text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing 2019-01-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 20 20 20 20 20 20 20 20 0 0 0 0 0 0 0 0 19 1 19 0 0 19 0 0 0 20 0 0 0 0 0 0 19 19 19 0 3898014 4015573 37698 42095 648268 915282 47636 69828 103365 105214 7778 7953 4649647 5036069 93112 119876 -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 -trimmer trimmer Trim leading or trailing characters. To update Text Manipulation trimmer 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 5304 7438 447 512 15698 108672 658 2946 266 822 53 81 21268 116932 1158 3539 -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 -varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 2013-11-17 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5058 6139 606 699 17232 53268 2965 5686 2298 2656 424 482 24588 62063 3995 6867 -vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 221 57 65 1399 2700 209 584 0 0 0 0 1590 2921 266 649 -vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 263 340 31 54 263 342 31 56 -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 513 569 6 9 513 569 6 9 -vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 400 455 129 140 0 0 0 0 238 606 19 56 638 1061 148 196 -vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 3 0 0 0 0 335 463 19 28 335 482 19 31 -vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 192 81 90 1853 3943 581 1280 144 156 13 16 2152 4291 675 1386 -vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 440 594 127 142 0 0 0 0 0 16 0 12 440 610 127 154 -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus 2016-10-16 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -vcftools_isec vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 537 104 118 0 1 0 1 39 496 28 48 418 1034 132 167 -vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 817 1084 244 273 0 0 0 0 93 448 44 60 910 1532 288 333 -vcftools_slice vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 423 56 60 6261 8115 133 362 127 157 10 19 6798 8695 199 441 -vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 142 46 49 0 0 0 0 120 142 12 19 254 284 58 68 -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 -add_input_name_as_column addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column 2020-03-24 mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 76834 86002 227 246 20174 20953 312 395 11 11 2 2 97019 106966 541 643 -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 -allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro 2017-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 -bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx 2015-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 131 15 20 329 785 50 210 0 0 0 0 412 916 65 230 -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 -basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil 2019-05-22 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 306 311 82 83 467 467 99 99 0 0 0 0 773 778 181 182 -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 -bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://www.encodeproject.org/software/bedgraphtobigwig/ Convert Formats bbgbigwig 2024-06-14 iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig 0.1 ucsc-bedgraphtobigwig 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 7 7 175 175 26 26 0 0 0 0 217 217 33 33 -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 -bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.21 Data handling, Variant calling DNA polymorphism, GWAS study, Genotyping experiment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 2023-08-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 33 33 9 9 0 0 0 0 0 0 0 0 33 33 9 9 -beacon2-import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://pypi.org/project/beacon2-import/ Variant Analysis Beacon2_Import 2024-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import 2.2.4 beacon2-import 2.2.4 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 12 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 7 7 0 0 0 0 0 0 0 0 22 22 7 7 -beagle beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle 2021-07-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 28 28 0 0 0 0 0 0 0 0 88 88 28 28 -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed 2023-08-08 iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 36 36 181 181 62 62 0 0 0 0 274 274 98 98 -bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 Mapping Genomics 37 37 37 37 37 37 37 37 0 0 0 0 0 0 0 0 37 6 37 0 0 37 0 0 0 37 0 0 0 0 0 0 37 37 37 0 916111 962278 13235 14525 407944 647621 25849 41751 84008 89233 2486 2832 1408063 1699132 41570 59108 -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers 2018-04-23 iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.9 python-bioext 0.21.9 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 17413 17413 822 822 15349 15349 2020 2020 2 2 1 1 32764 32764 2843 2843 -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast 2022-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 738 738 151 151 0 0 0 0 2 2 1 1 740 740 152 152 -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 -bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 2018-04-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 Read mapping Mapping, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 397893 427447 12133 13176 577209 903193 33086 52020 60105 67495 3779 4271 1035207 1398135 48998 69467 -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 -breseq breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq 2019-10-21 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.39.0 Polymorphism detection Sequencing, Sequence analysis, DNA mutation 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 2976 2976 98 98 0 0 0 0 884 884 70 70 3860 3860 168 168 -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 -bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa 2017-11-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 2 976935 1017671 13526 14401 474702 681286 32627 47624 79802 87191 4219 4954 1531439 1786148 50372 66979 -bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 2021-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 Sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 56619 56619 2324 2324 36631 36631 2808 2808 18121 18121 713 713 111371 111371 5845 5845 -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param 2021-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1393 1393 10 10 0 0 0 0 0 0 0 0 1393 1393 10 10 -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 -chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca 2024-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.10 0 0 8 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 727 727 76 76 0 0 0 0 0 0 0 0 727 727 76 76 -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 -circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos 2020-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 Sequence visualisation 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 26265 26265 2483 2483 31332 31332 3535 3535 26359 26359 999 999 83956 83956 7017 7017 -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 -cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 -cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.1.0 cnv-vcf2json 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit 2023-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 Variant calling 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 618 618 177 177 0 0 0 0 0 0 0 0 618 618 177 177 -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 -collection_column_join collection_column_join Column Join on Collections To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join Text Manipulation collection_column_join 2016-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 23979 25337 3827 4011 21671 25163 4645 5045 2939 3036 688 701 48589 53536 9160 9757 -collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers Text Manipulation collection_element_identifiers 2018-06-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6905 7102 1620 1630 7761 7761 1897 1897 1157 1157 243 243 15823 16020 3760 3770 -column_maker Add_a_column1 Compute an expression on every row To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker Text Manipulation column_maker 2019-06-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2940752 3907183 5422 6121 263254 737503 6095 13728 96478 97667 884 974 3300484 4742353 12401 20823 -column_order_header_sort column_order_header_sort Sort Column Order by heading To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort Text Manipulation column_order_header_sort 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3735 3891 268 297 1923 1923 381 381 0 0 0 0 5658 5814 649 678 -column_remove_by_header column_remove_by_header Remove columns by header To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header Text Manipulation column_remove_by_header 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8331 8917 613 662 5206 5206 716 716 1976 1976 27 27 15513 16099 1356 1405 -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 -compose_text_param compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param 2019-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 45827 45831 689 691 7721 7721 303 303 1481 1481 121 121 55029 55033 1113 1115 -compress_file compress_file Compress files. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file Text Manipulation compress_file 2022-02-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6343 6343 290 290 3674 3674 286 286 11832 11832 59 59 21849 21849 635 635 -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies Up-to-date http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap 2017-07-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.7.0 crossmap 0.7.0 5 0 6 0 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 2182 2182 331 331 5251 5251 903 903 0 0 0 0 7433 7433 1234 1234 -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 -cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Up-to-date https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv 2020-09-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 2.1.1 cutesv 2.1.1 Split read mapping, Genotyping, Structural variation detection Sequencing, Computer science 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 260 260 43 43 0 0 0 0 119 119 8 8 379 379 51 51 -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 173 280 41 83 0 0 0 0 173 280 41 83 -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga 2016-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation 2015-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 1 3 3 0 0 1 0 0 0 1 0 0 0 0 0 0 3 3 3 0 748586 760943 7066 7307 98089 112831 5306 6131 16235 16317 2161 2171 862910 890091 14533 15609 -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 -deepvariant deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant 2021-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2561 2561 325 325 2916 2916 460 460 0 0 0 0 5477 5477 785 785 -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly 2020-10-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.3.1 Indel detection, Structural variation detection, Genotyping Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 1451 1451 288 288 0 0 0 0 0 0 0 0 1451 1451 288 288 -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 -diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq Up-to-date http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2018-04-07 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 3.12.0 bioconductor-diffbind 3.12.0 Differential binding analysis ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7092 7663 606 652 14367 18624 1360 1916 1477 1640 69 84 22936 27927 2035 2652 -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot 2022-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver 2022-12-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 -ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools 2016-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.1 six 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 406 133 163 1421 1421 547 547 0 0 0 0 1697 1827 680 710 -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 -ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload 2020-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.3 ena-upload-cli 0.7.4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 366 366 41 41 0 0 0 0 1302 1302 14 14 1668 1668 55 55 -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch 2017-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1989 2302 367 453 0 0 0 0 0 0 0 0 1989 2302 367 453 -ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep 2022-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 112.0 ensembl-vep 113.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3051 3051 171 171 0 0 0 0 0 0 0 0 3051 3051 171 171 -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 -extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna 2016-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 9409 12735 813 923 20180 259099 2072 11791 168 611 20 63 29757 272445 2905 12777 -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf 2023-01-11 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 385 385 46 46 587 587 107 107 58 58 5 5 1030 1030 158 158 -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 -freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Up-to-date https://github.com/ekg/freebayes Variant Analysis freebayes 2017-01-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.8 freebayes 1.3.8 Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 149715 171093 8158 8794 144708 256315 15996 25107 19156 21936 2251 2571 313579 449344 26405 36472 -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec 2020-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk Copy number estimation, Variant calling, Genome alignment Oncology, Human genetics, Data mining 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 748 748 91 91 0 0 0 0 12 12 1 1 760 760 92 92 -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution 2019-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 578 578 34 34 0 0 0 0 578 578 34 34 -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 2019-10-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3463 3463 452 452 9040 9040 1639 1639 0 0 0 0 12503 12503 2091 2091 -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp 2017-06-23 iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 -genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta 2020-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 4 4 2 2 221 2905 23 279 0 0 0 0 225 2909 25 281 -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 Variant Analysis genehunter_modscore 2017-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 660 104 197 0 0 0 0 445 660 104 197 -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 -genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich 2019-07-05 iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3534 3577 402 405 2840 2840 419 419 571 571 31 31 6945 6988 852 855 -get_hrun get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 -gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9664 9775 763 765 5623 5623 493 493 1000 1000 135 135 16287 16398 1391 1393 -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset 2022-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 2018-05-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8329 9363 3336 3828 8009 8009 3130 3130 1577 1577 344 344 17915 18949 6810 7302 -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 -gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. To update https://github.com/sequencing/gvcftools Variant Analysis 2016-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy 2022-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 -hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard To update https://github.com/VariantEffect/hgvsParseR/tree/master Variant Analysis hgvsparser 2024-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6346 6346 2 2 0 0 0 0 0 0 0 0 6346 6346 2 2 -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.8.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids 2020-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.45 omero-py 5.11.1 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 404 404 37 37 0 0 0 0 24 24 1 1 428 428 38 38 -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 -intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter To update https://github.com/intermine Convert Formats intermine_galaxy_exchange 2018-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 6 12 72 87 13 15 108 108 1 1 217 241 20 28 -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 -interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf 2020-07-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.13.0 Sequence analysis 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 107 7 10 758 19538 87 1246 16 24 2 2 806 19669 96 1258 -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 -irissv irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.21 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 -jasminesv jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 9 9 53 53 19 19 0 0 0 0 85 85 28 28 -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id Text Manipulation join_files_by_id 2017-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -jq jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 660 2374 61 63 336 336 82 82 281 281 11 11 1277 2991 154 156 -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit 2021-02-11 iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7179 7179 509 509 11138 11138 1145 1145 0 0 0 0 18317 18317 1654 1654 -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 -king king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king 2021-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.4.14 kma 1.4.15 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 -lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz 2018-02-19 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 Sequence alignment, Read mapping Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 77409 84356 447 475 156658 193590 870 3511 38579 38780 173 203 272646 316726 1490 4189 -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie 2022-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis 2019-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 5 5 5 4 5 5 5 4 0 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4176367 4176367 4301 4301 509615 509615 8213 8213 106342 106342 1815 1815 4792324 4792324 14329 14329 -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 -lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv 2020-11-12 iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1534 1534 199 199 0 0 0 0 0 0 0 0 1534 1534 199 199 -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 -maf_stats maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats 2020-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 15 21 7 9 227 2470 52 464 1 1 1 1 243 2492 60 474 -maftoaxt maftoaxt Convert dataset from MAF to axt format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_maftoaxt 2024-07-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt 469 ucsc-maftoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing 2018-03-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 Genetic variation analysis Genetics, Genetic variation, Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 11761 12093 873 889 5762 5762 473 473 5610 5610 343 343 23133 23465 1689 1705 -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run 2021-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 9 9 0 0 0 0 0 0 0 0 24 24 9 9 -map_param_value map_param_value Map a parameter value to another value To update Text Manipulation map_param_value 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3780 3780 67 67 1012 1012 57 57 105 105 3 3 4897 4897 127 127 -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme 2018-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.5.6 meme 5.5.7 Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability 3 0 4 0 3 0 4 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 20990 22979 762 892 10975 25929 1551 3249 0 0 0 0 31965 48908 2313 4141 -meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip 2018-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6413 7000 705 743 7260 7260 1171 1171 0 0 0 0 13673 14260 1876 1914 -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin 2020-04-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 Haplotype mapping GWAS study, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 -minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 2018-08-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 Pairwise sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 346530 349075 4323 4419 108535 108535 4075 4075 22331 22331 1166 1166 477396 479941 9564 9660 -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 -moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs 2019-07-28 iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 339 339 56 56 0 0 0 0 0 0 0 0 339 339 56 56 -mosdepth mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth 2022-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1278 1278 87 87 168 168 24 24 102 102 5 5 1548 1548 116 116 -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps 2017-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 485 871 159 298 0 0 0 0 485 871 159 298 -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 -ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download 2019-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6873 6873 1664 1664 17651 17651 4513 4513 6228 6228 972 972 30752 30752 7149 7149 -ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.20.0 ncbi-datasets-cli Data handling, Sequence database search, Data retrieval Biological databases 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4417 4417 1024 1024 6940 6940 2275 2275 1 1 1 1 11358 11358 3300 3300 -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct 2022-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 22.4 entrez-direct 22.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 3 0 2 -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils 2020-08-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 4 0 0 4 0 0 0 2 0 0 0 0 0 0 0 7 7 0 2794 3191 533 664 0 0 0 0 0 0 0 0 2794 3191 533 664 -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 -ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr 2020-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1403 1403 49 49 0 0 0 0 0 0 0 0 1403 1403 49 49 -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM 2015-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24611 29662 633 716 15523 21395 740 1128 7751 8972 125 145 47885 60029 1498 1989 -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 -ococo ococo Variant detection of SNVs To update https://github.com/karel-brinda/ococo Variant Analysis ococo 2017-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1850 1963 79 93 1370 1370 194 194 0 0 0 0 3220 3333 273 287 -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit 2017-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 582 663 68 69 0 0 0 0 0 0 0 0 582 663 68 69 -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe 2022-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader Data Source packaged_annotation_loader 2022-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp 2022-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 Variant calling Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 2022-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.14.99 pbmm2 1.14.99 Pairwise sequence alignment, Sorting Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 17 17 0 0 0 0 0 0 0 0 70 70 17 17 -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 -pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram 2016-06-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.2 openjdk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5505 5505 510 510 7932 8582 811 909 736 736 119 119 14173 14823 1440 1538 -peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla 2024-02-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 -picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard 2019-05-30 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.3.0 Formatting Sequencing 31 31 31 31 31 31 31 31 0 0 0 0 0 0 0 0 31 4 31 0 0 31 0 0 0 31 0 0 0 0 0 0 31 31 31 0 386934 399039 11024 11956 366646 589980 32000 57111 56622 62258 2845 3398 810202 1051277 45869 72465 -pick_value pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value 2023-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1607 1607 41 41 490 490 53 53 127 127 4 4 2224 2224 98 98 -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 -pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update https://github.com/broadinstitute/pilon/wiki Variant Analysis pilon 2016-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 Sequence assembly, Analysis Assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9045 9458 1115 1144 7989 7989 1070 1070 3945 4137 726 741 20979 21584 2911 2955 -pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign 2019-08-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1245 1245 231 231 9046 9046 630 630 0 0 0 0 10291 10291 861 861 -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 -plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink 2020-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 Genetic variation analysis GWAS study 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 851 851 127 127 249 249 43 43 0 0 0 0 1100 1100 170 170 -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2716 2716 104 104 134 134 43 43 40 40 1 1 2890 2890 148 148 -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 -query_impc query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc 2023-10-11 iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 -query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular Text Manipulation 2017-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.1 python 3 3 3 1 3 3 3 1 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 130124 135361 1265 1305 11135 11135 922 922 5939 5939 153 153 147198 152435 2340 2380 -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 415 721 128 219 0 0 0 0 415 721 128 219 -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3543 3619 108 111 536 536 157 157 0 0 0 0 4079 4155 265 268 -resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window 2016-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 86 8 9 138 216 30 57 0 0 0 0 213 302 38 66 -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor 2023-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths 2022-10-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign 2022-03-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba 2022-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools 2022-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser 2022-06-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -samtools To update https://github.com/samtools/samtools SAM 2021-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.20 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa 2020-12-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.2 sansa 0.2.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 138 138 36 36 0 0 0 0 0 0 0 0 138 138 36 36 -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol 2022-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 -seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr 2020-02-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5106 5106 116 116 6419 6419 241 241 0 0 0 0 11525 11525 357 357 -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext 2021-02-28 iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 0 2 4 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 220 220 68 68 0 0 0 0 416 416 10 10 636 636 78 78 -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists 2019-10-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6555 6555 807 807 5336 5336 171 171 1143 1143 182 182 13034 13034 1160 1160 -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites 2017-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6597 6597 663 663 1467 1467 256 256 1279 1279 114 114 9343 9343 1033 1033 -snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff 2018-07-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 5 5 5 5 5 5 5 5 0 0 0 0 0 1 0 0 0 5 5 0 0 5 0 0 0 5 0 0 0 0 0 0 5 5 5 0 103826 108296 7181 7908 115727 178110 15871 22769 11817 13155 2148 2321 231370 299561 25200 32998 -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 SNP detection DNA polymorphism, Nucleic acid sites, features and motifs 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 764895 764895 1276 1276 94572 94572 1636 1636 26990 26990 561 561 886457 886457 3473 3473 -snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region To update https://github.com/BrownfieldPlantLab/SNPFreqPlot Variant Analysis snpfreqplot 2020-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 3683 3683 338 338 1401 1401 433 433 1029 1029 95 95 6113 6113 866 866 -snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift 2015-04-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 8 8 8 8 8 8 8 8 0 0 0 0 0 8 0 0 0 0 8 0 0 8 0 0 0 8 0 0 0 0 0 0 8 8 8 0 5142904 5146618 3602 4283 382391 421190 7013 9678 104030 105024 960 1184 5629325 5672832 11575 15145 -snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 52 55 23 24 421 421 75 75 0 0 0 0 473 476 98 99 -snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 509 554 107 128 474 474 190 190 0 0 0 0 983 1028 297 318 -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign 2022-10-02 iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka 2021-01-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 669 669 112 112 1261 1261 417 417 0 0 0 0 1930 1930 529 529 -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink 2017-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 -table_compute table_compute Perform general-purpose table operations To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute Text Manipulation table_compute 2019-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 216072 216115 1811 1814 12326 12326 1558 1558 16136 16136 256 256 244534 244577 3625 3628 -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 -tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter 2019-10-03 iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22977 22977 461 461 3888 3888 274 274 3611 3611 80 80 30476 30476 815 815 -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 -tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.1 tbvcfreport 1.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2955 2955 335 335 6090 6090 348 348 2347 2347 72 72 11392 11392 755 755 -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update 2021-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.8 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 3314 3314 124 124 0 0 0 0 0 0 0 0 3314 3314 124 124 -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 -tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 255 379 31 37 281 281 64 64 0 0 0 0 536 660 95 101 -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa 2016-08-19 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 469 ucsc-twobittofa 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 413 511 84 118 441 441 123 123 21 21 2 2 875 973 209 243 -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_axttomaf 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf 469 ucsc-axttomaf 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_nettoaxt 2024-09-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt 469 ucsc-nettoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java 2020-08-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 381 381 37 37 0 0 0 0 0 0 0 0 381 381 37 37 -variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer 2019-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 95 95 14 14 516 516 67 67 0 0 0 0 611 611 81 81 -varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan 2018-11-29 iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 10711 11502 1442 1560 16705 16705 3135 3135 1036 1036 100 100 28452 29243 4677 4795 -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 -vcf2maf vcf2maf vcf2maf: Convert VCF into MAF To update https://github.com/mskcc/vcf2maf Convert Formats vcf2maf 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1097 1097 46 46 0 0 0 0 65 65 5 5 1162 1162 51 51 -vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 169090 169679 823 874 16304 42215 1141 2594 2485 2511 169 172 187879 214405 2133 3640 -vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 882 888 30 32 6118 8261 36 114 175 184 6 6 7175 9333 72 152 -vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6879 17157 897 1219 7585 14509 1245 1925 1648 1681 225 229 16112 33347 2367 3373 -vcfanno vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 SNP annotation Genetic variation, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1139 1139 174 174 0 0 0 0 0 0 0 0 1139 1139 174 174 -vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2797 2850 157 181 3668 14532 652 1392 494 507 61 63 6959 17889 870 1636 -vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 203 62 66 497 1828 155 387 184 197 11 11 870 2228 228 464 -vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3017 4049 185 210 4709 20250 406 1147 507 527 40 42 8233 24826 631 1399 -vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 416 478 35 40 3969 10457 82 309 362 378 8 8 4747 11313 125 357 -vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 767 96 106 803 1895 222 627 241 256 16 17 1789 2918 334 750 -vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1422 2020 284 505 4951 19530 1021 2669 493 516 60 62 6866 22066 1365 3236 -vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 233 253 37 42 234 1839 79 287 199 214 11 12 666 2306 127 341 -vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 572 585 90 92 2063 2427 139 296 272 290 19 22 2907 3302 248 410 -vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37489 47142 2113 2218 75128 162296 5730 10533 2626 2736 320 331 115243 212174 8163 13082 -vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 926 957 155 173 2291 5323 313 985 251 265 28 31 3468 6545 496 1189 -vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 172 183 21 25 351 879 67 201 312 342 15 16 835 1404 103 242 -vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 778 794 107 112 2414 3721 179 508 209 225 20 21 3401 4740 306 641 -vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 502 555 134 143 3428 6338 266 858 220 235 23 24 4150 7128 423 1025 -vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1964 1991 182 186 1937 3846 188 644 567 601 26 27 4468 6438 396 857 -vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 269 310 38 42 358 1071 89 287 179 213 12 14 806 1594 139 343 -vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 711 28 33 403 831 75 200 190 214 10 12 1183 1756 113 245 -vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 168 13 15 153 350 27 75 184 192 6 6 498 710 46 96 -vcfselectsamples vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 830 900 69 88 1315 6257 237 959 344 363 20 21 2489 7520 326 1068 -vcfsort vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1868 1904 174 185 18378 24175 422 1279 537 674 70 73 20783 26753 666 1537 -vcfvcfintersect vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 976544 977015 703 748 64155 81830 981 2103 11044 11069 225 229 1051743 1069914 1909 3080 -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -weblogo3 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 2017-11-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2720 2818 206 228 10299 30578 1354 3657 1226 1285 50 59 14245 34681 1610 3944 -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig 2024-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 469 ucsc-wigtobigwig 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1601 1601 106 106 1108 1108 172 172 200 200 15 15 2909 2909 293 293 -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 -winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap 2021-04-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 279 279 46 46 12 12 4 4 0 0 0 0 291 291 50 50 -xpath xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 235 7 8 0 1 0 1 0 0 0 0 128 236 7 9 -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 -zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 96 9 12 0 0 0 0 0 0 0 0 83 96 9 12 -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq 2021-10-08 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49465 49465 281 281 0 0 0 0 0 0 0 0 49465 49465 281 281 -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 -appendfdr append_fdr To update appendfdr 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning 2020-10-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -astropytools astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations To update https://github.com/astropy/astropy Astronomy astropytools 2023-04-11 volodymyrss https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0.1.0+galaxy0 astropy 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 5 5 0 0 0 0 0 0 0 0 13 13 5 5 -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 -bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph 2021-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 469 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig 2018-09-25 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 469 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 -c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s 2021-04-13 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.3.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 234 234 11 11 4 4 4 4 92 92 3 3 330 330 18 18 -cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads 2021-06-19 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 1 1 0 0 0 0 0 0 0 0 52 52 1 1 -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis 2021-09-01 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 218 218 17 17 0 0 0 0 0 0 0 0 218 218 17 17 -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 -cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm 2021-06-15 climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 2 2 0 0 0 0 0 0 0 0 14 14 2 2 -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets 2019-04-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 4822 4824 613 614 1317 1317 204 204 3088 3795 252 289 9227 9936 1069 1107 -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler 2018-12-07 lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.21 4 0 5 0 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 170 170 26 26 195 195 39 39 0 0 0 0 365 365 65 65 -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -cta cta_astro_tool Basic simulation of CTA telescope observations using gammapy package To update Astronomy cta_astro_tool 2024-04-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0.0.1+galaxy0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 -digestdb digestdb To update digestdb 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -directag_and_tagrecon To update directag_and_tagrecon 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa 2022-11-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 -eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie 2021-12-30 climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 4 4 0 0 0 0 0 0 0 0 45 45 4 4 -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability 2019-05-03 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 336 39 40 0 0 0 0 0 0 0 0 232 336 39 40 -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates 2020-10-21 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 264 264 69 69 34 34 11 11 103 103 1 1 401 401 81 81 -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox 2018-06-05 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 2019-07-31 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 2021-12-29 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage 2018-06-13 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed 2018-01-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 2230 329 347 1071 1071 362 362 492 492 64 64 2938 3793 755 773 -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 -hess hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope To update Astronomy hess_astro_tool 2024-02-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0.0.2+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff 2017-09-27 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip 2018-05-16 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ltq_iquant_cli To update ltq_iquant_cli 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove 2020-07-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 1.3 lumpy-sv 0.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 -manta manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta 2023-06-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 218 218 34 34 0 0 0 0 0 0 0 0 218 218 34 34 -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 -mgf_formatter mgf_formatter Up-to-date mgf_formatter 2014-09-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns 2020-10-19 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel 2021-09-29 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment 2016-11-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment 2016-11-07 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 -protxml_to_xls protxml_to_xls To update protxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -psm_eval psm_eval To update psm_eval 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 -pyvo_integration astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy To update Data Source astronomicalarchivestool 2023-08-26 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0.10.0 astropy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 6 6 0 0 0 0 0 0 0 0 53 53 6 6 -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 -query query Execute an SQL statement on a set of tables To update Text Manipulation query 2020-12-09 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 -regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace 2017-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 78648 78834 1144 1156 18063 18063 870 870 4455 6051 194 289 101166 102948 2208 2315 -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam 2019-04-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.21 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 11 11 520 520 31 31 0 0 0 0 560 560 42 42 -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba 2020-05-19 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 684 684 17 17 684 684 17 17 -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 -scaffold scaffold, scaffold_export To update scaffold 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 -scripting singularity_scriptrunner suite_scripting To update https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ Text Manipulation scripting tools 2023-07-29 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 -sgwb sgwb_astro_tool SGWB To update Astronomy sgwb_astro_tool 2024-04-17 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0.0.1+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 0 0 0 0 0 0 0 0 5 5 2 2 -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 64 4 4 0 0 0 0 0 0 0 0 54 64 4 4 -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes 2019-04-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv 2021-03-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf 2022-11-28 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 -xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet 2021-10-18 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 17 17 0 0 0 0 0 0 0 0 59 59 17 17 -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 diff --git a/communities/assembly/resources/tools.tsv b/communities/assembly/resources/tools.tsv deleted file mode 100644 index 68169210..00000000 --- a/communities/assembly/resources/tools.tsv +++ /dev/null @@ -1,178 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False +Galaxy wrapper id Description To keep Deprecated +TrimNs TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline +abacas Order and Orientate Contigs +abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. +agat GTF/GFF analysis toolkit +align_back_trans Thread nucleotides onto a protein alignment (back-translation) +assembly-stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. +assemblystats Summarise an assembly (e.g. N50 metrics) +atactk_trim_adapters Trim adapters from paired-end HTS reads. +bam2mappingstats Generates mapping stats from a bam file. +barcode_splitter A utility to split sequence files using multiple sets of barcodes +berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. +bionano Bionano Solve is a set of tools for analyzing Bionano data +biscot Bionano scaffolding correction tool +blast_rbh BLAST Reciprocal Best Hits (RBH) from two FASTA files +blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs +blast_unmatched Extract unmatched query sequences from blast +blastparser_and_hits Parse blast outputs and compile hits +blastx_to_scaffold Generate DNA scaffold from blastx alignment of Contigs +blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. +cap3 cap3 wrapper +cdhit Cluster or compare biological sequence datasets +cherry_pick_fasta Pick fasta sequence with specific header content +circexplorer2 Comprehensive and integrative circular RNA analysis toolset. +clc_assembly_cell Galaxy wrapper for the CLC Assembly Cell suite from CLCBio +combine_assembly_stats Combine multiple Assemblystats datasets into a single tabular report +convert_solid_color2nuc Convert Color Space to Nucleotides +count_roi_variants Count sequence variants in region of interest in BAM file +coverage_stats BAM coverage statistics using samtools idxstats and depth +cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). +disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler +ear A tool to compile assembly reports and stastics from assembly pipeline +emboss_5 Galaxy wrappers for EMBOSS version 5.0.0 tools +fasplit faSplit is a tool to split a single FASTA file into several files +fasta_clipping_histogram Length Distribution chart +fasta_compute_length Compute sequence length +fasta_concatenate_by_species Concatenate FASTA alignment by species +fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) +fasta_filter_by_length Filter sequences by length +fasta_formatter FASTA Width formatter +fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together +fasta_nucleotide_changer RNA/DNA converter. +fasta_to_tabular FASTA-to-Tabular converter +fastk FastK: A K-mer counter (for HQ assembly data sets) +fastq_combiner Combine FASTA and QUAL into FASTQ +fastq_filter Filter FASTQ reads by quality score and length +fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) +fastq_groomer Convert between various FASTQ quality formats. +fastq_info FASTQ info allows to validate single or paired fastq files +fastq_manipulation Manipulate FASTQ reads on various attributes. +fastq_masker_by_quality FASTQ Masker by quality score +fastq_pair Paired-end fastq pairer +fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. +fastq_paired_end_interlacer FASTQ interlacer on paired end reads +fastq_paired_end_joiner FASTQ joiner on paired end reads +fastq_paired_end_splitter FASTQ splitter on joined paired end reads +fastq_quality_boxplot Draw quality score boxplot +fastq_quality_converter Quality format converter (ASCII-Numeric) +fastq_quality_filter Filter by quality +fastq_quality_trimmer FASTQ trimmer based on quality +fastq_stats FASTQ Summary Statistics by column +fastq_to_fasta FASTQ to FASTA converter +fastq_to_tabular FASTQ to Tabular converter +fastq_trimmer FASTQ Trimmer by quality +fastq_trimmer_by_quality FASTQ Quality Trimmer by sliding window +fastqc Read QC reports using FastQC +fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data +fastqtofasta FASTQ to FASTA converter +fastx_artifacts_filter Remove sequencing artifacts +fastx_barcode_splitter Barcode Splitter +fastx_clipper Clip adapter sequences +fastx_collapser Collapse sequences +fastx_nucleotides_distribution Draw nucleotides distribution chart +fastx_quality_statistics Compute quality statistics +fastx_renamer Rename sequences +fastx_reverse_complement Reverse-Complement +fastx_trimmer Trim sequences +fermikit FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. +fetch_fasta_from_ncbi Fetch fasta sequences from NCBI using eutils wrappers +filter_by_fasta_ids Filter FASTA on the headers and/or the sequences +filter_spades_repeats Remove short and repeat contigs/scaffolds +filtlong Filtlong - Filtering long reads by quality +flair FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. +flash Fast Length Adjustment of SHort reads +flye Assembly of long and error-prone reads. +format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file +get_pairs Separate paired and unpaired reads from two fastq files +get_reference_fasta Obtain reference genome sequence. +getorganelle GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. +graphmap Mapper for long, error-prone reads. +guppy A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies +hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies +hapog Hapo-G - Haplotype-Aware Polishing of Genomes +hifiasm A fast haplotype-resolved de novo assembler +hisat HISAT is a fast and sensitive spliced alignment program. +hisat2 HISAT2 is a fast and sensitive spliced alignment program. +hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies +idba_ud Wrappers for the idba assembler variants. +instagraal Large genome reassembly based on Hi-C data +jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA +khmer In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more +length_and_gc_content Gets gene length and gc content from a fasta and a GTF file +lighter Lighter is a kmer-based error correction method for whole genome sequencing data +links Scaffold genome assemblies with long reads. +make_nr Make a FASTA file non-redundant +megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. +megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) +merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. +meryl Meryl a k-mer counter. +mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. +minia Short-read assembler based on a de Bruijn graph +miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) +mitobim assemble mitochondrial genomes +mitohifi Assembly mitogenomes from Pacbio HiFi read. +msaboot A multiple sequences alignment bootstrapping tool. +multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report +necat Error correction and de-novo assembly for ONT Nanopore reads +nextdenovo String graph-based de novo assembler for long reads +nlstradamus Find nuclear localization signals (NLSs) in protein sequences +novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. +oases Short read assembler +ont_fast5_api ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. +pbtk Convert PacBio Bam File to fasta or fastq file +pear PEAR evaluates all possible paired-end read overlaps +plasmidspades Genome assembler for assemblying plasmid +porechop Porechop - Finding and removing adapters from Oxford Nanopore reads +poretools A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. +prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets +promer Aligns two sets of contigs and reports amino acid substitutions between them +purge_dups Purge haplotigs and overlaps in an assembly based on read depth +pycoqc QC metrics for ONT Basecalling +qfilt Filter sequencing data +quast Quast (Quality ASsessment Tool) evaluates genome assemblies. +quickmerge Merge long-read and hybrid assemblies to increase contiguity +ragtag Reference-guided scaffolding of draft genomes tool. +raven Raven is a de novo genome assembler for long uncorrected reads. +rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. +rnaquast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. +salsa2 A tool to scaffold long read assemblies with Hi-C +samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files +sample_seqs Sub-sample sequences files (e.g. to reduce coverage) +samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) +samtools_depth Coverage depth via samtools +samtools_idxstats BAM mapping statistics (using samtools idxstats) +seq_filter_by_id Filter sequences by ID +seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files +seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) +seq_primer_clip Trim off 5' or 3' primers +seq_rename Rename sequences with ID mapping from a tabular file +seq_select_by_id Select sequences by ID +seqprep Tool for merging paired-end Illumina reads and trimming adapters. +sequence_format_converter various fasta to tabular conversions +shasta Fast de novo assembly of long read sequencing data +short_reads_trim_seq Select high quality segments +shovill Faster de novo assembly pipeline based around Spades +sickle A windowed adaptive trimming tool for FASTQ files using quality +smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing +spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. +spades_header_fixer Fixes Spades Fasta ids +split_paired_reads Split paired end reads +sra-tools NCBI Sequence Read Archive toolkit utilities +tabular_to_fastq Tabular to FASTQ converter +tarfast5 produces a tar.gz archive of fast5 sequence files +taxonomy_krona_chart Krona pie chart from taxonomic profile +tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. +trim_galore Trim Galore adaptive quality and adapter trimmer +trimmomatic A flexible read trimming tool for Illumina NGS data +trycycler Trycycler toolkit wrappers +unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. +validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. +velvet de novo genomic assembler specially designed for short read sequencing technologies +velvet_optimiser Automatically optimize Velvet assemblies +verkko Telomere-to-telomere assembly pipeline +wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. +xpore Identification and quantification of differential RNA modifications from direct RNA sequencing +yac_clipper Clips 3' adapters for small RNA sequencing reads. +yahs Yet Another Hi-C scaffolding tool diff --git a/communities/biodiversity/metadata/tool_status.tsv b/communities/biodiversity/metadata/tool_status.tsv deleted file mode 100644 index e69de29b..00000000 diff --git a/communities/biodiversity/resources/tools.tsv b/communities/biodiversity/resources/tools.tsv deleted file mode 100644 index 39e16729..00000000 --- a/communities/biodiversity/resources/tools.tsv +++ /dev/null @@ -1,134 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False diff --git a/communities/biodiversity/resources/tools_filtered_by_ts_categories.json b/communities/biodiversity/resources/tools_filtered_by_ts_categories.json new file mode 100644 index 00000000..0e78c86f --- /dev/null +++ b/communities/biodiversity/resources/tools_filtered_by_ts_categories.json @@ -0,0 +1,11975 @@ +[ + { + "Galaxy wrapper id": "braker", + "Galaxy tool ids": [ + "braker" + ], + "Description": "BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Gaius-Augustus/BRAKER", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "braker", + "Date of first commit of the suite": "2021-10-05", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", + "Galaxy wrapper version": "2.1.6", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0, + "Tools available on Viral Variant Visualizer (VVV)": 0, + "No. of tool users (5 years) (usegalaxy.eu)": 165, + "No. of tool users (all time) (usegalaxy.eu)": 165, + "Tool usage (5 years) (usegalaxy.eu)": 48, + "Tool usage (all time) (usegalaxy.eu)": 48, + "No. of tool users (5 years) (usegalaxy.org)": 0, + "No. of tool users (all time) (usegalaxy.org)": 0, + "Tool usage (5 years) (usegalaxy.org)": 0, + "Tool usage (all time) (usegalaxy.org)": 0, + "No. of tool users (5 years) (usegalaxy.org.au)": 0, + "No. of tool users (all time) (usegalaxy.org.au)": 0, + "Tool usage (5 years) (usegalaxy.org.au)": 0, + "Tool usage (all time) (usegalaxy.org.au)": 0, + "No. of tool users (5 years) - 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False +Galaxy wrapper id Description To keep Deprecated +EMLassemblyline Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa +Ecoregionalization_workflow Tools to compute ecoregionalization with BRT model predictions and clustering. +Geom_mean_workflow Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). +PAMPA Tools to compute and analyse biodiversity metrics +TrimNs TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline +abacas Order and Orientate Contigs +abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages +aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. +aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. +argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database +assembly-stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. +assemblystats Summarise an assembly (e.g. N50 metrics) +bam2mappingstats Generates mapping stats from a bam file. +baseline_calculator Toxicity prediction using QSAR models +bionano Bionano Solve is a set of tools for analyzing Bionano data +biotradis Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. +biscot Bionano scaffolding correction tool +blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs +blastparser_and_hits Parse blast outputs and compile hits +blastx_to_scaffold Generate DNA scaffold from blastx alignment of Contigs +blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. +braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . +braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . +cap3 cap3 wrapper +champ_blocs Compute indicators for turnover boulders fields +chipseeker A tool for ChIP peak annotation and visualization +circexplorer2 Comprehensive and integrative circular RNA analysis toolset. +clc_assembly_cell Galaxy wrapper for the CLC Assembly Cell suite from CLCBio +combine_assembly_stats Combine multiple Assemblystats datasets into a single tabular report +count_roi_variants Count sequence variants in region of interest in BAM file +coverage_stats BAM coverage statistics using samtools idxstats and depth +data_exploration Explore data through multiple statistical tools +deepsig Predictor of signal peptides in proteins based on deep learning +disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler +dose_responses A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses +ear A tool to compile assembly reports and stastics from assembly pipeline +evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. +fastk FastK: A K-mer counter (for HQ assembly data sets) +fermikit FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. +filter_spades_repeats Remove short and repeat contigs/scaffolds +flash Fast Length Adjustment of SHort reads +flye Assembly of long and error-prone reads. +funannotate Funannotate is a genome prediction, annotation, and comparison software package. +gdal Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. +getorganelle GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. +goenrichment Performs GO Enrichment analysis. +graphmap Mapper for long, error-prone reads. +hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies +hapog Hapo-G - Haplotype-Aware Polishing of Genomes +helixer Gene calling with Deep Neural Networks +hifiasm A fast haplotype-resolved de novo assembler +hirondelle_crim_ogc_api_processes This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. +hisat HISAT is a fast and sensitive spliced alignment program. +hisat2 HISAT2 is a fast and sensitive spliced alignment program. +hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies +icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. +idba_ud Wrappers for the idba assembler variants. +instagraal Large genome reassembly based on Hi-C data +interpolation Run IDW interpolation based on a .csv and .geojson file +jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA +khmer In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more +links Scaffold genome assemblies with long reads. +make_data_paper_sketches This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. +marine_omics The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data +mean-per-zone Creates a png image showing statistic over areas as defined in the vector file +medenv Retrieve environmental data from etopo, cmems and woa +megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. +megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) +merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. +meryl Meryl a k-mer counter. +metaeuk MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. +minia Short-read assembler based on a de Bruijn graph +miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) +mitobim assemble mitochondrial genomes +mitohifi Assembly mitogenomes from Pacbio HiFi read. +ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) +necat Error correction and de-novo assembly for ONT Nanopore reads +nextdenovo String graph-based de novo assembler for long reads +novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. +oases Short read assembler +obisindicators Compute biodiveristy indicators for marine data from obis +ocean Access, process, visualise oceanographic data for the Earth System +ogcProcess_otb_bandmath Outputs a monoband image which is the result of a mathematical operation on several multi-band images. +ogcProcess_otb_meanShiftSmoothing This application smooths an image using the MeanShift algorithm. +pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes +plasmidspades Genome assembler for assemblying plasmid +prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes +promer Aligns two sets of contigs and reports amino acid substitutions between them +purge_dups Purge haplotigs and overlaps in an assembly based on read depth +quast Quast (Quality ASsessment Tool) evaluates genome assemblies. +quickmerge Merge long-read and hybrid assemblies to increase contiguity +ragtag Reference-guided scaffolding of draft genomes tool. +raven Raven is a de novo genome assembler for long uncorrected reads. +regionalgam +repeatexplorer2 Tool for annotation of repeats from unassembled shotgun reads. +repeatmodeler RepeatModeler - Model repetitive DNA +retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers +rnaquast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. +salsa2 A tool to scaffold long read assemblies with Hi-C +sample_seqs Sub-sample sequences files (e.g. to reduce coverage) +samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) +samtools_depth Coverage depth via samtools +samtools_idxstats BAM mapping statistics (using samtools idxstats) +sdmpredictors Terrestrial and marine predictors for species distribution modelling. +seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files +seq_primer_clip Trim off 5' or 3' primers +shasta Fast de novo assembly of long read sequencing data +shovill Faster de novo assembly pipeline based around Spades +smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing +spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. +spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. +spocc Get species occurences data +srs_tools Compute biodiversity indicators for remote sensing data from Sentinel 2 +stoc Tools to analyse STOC data. +taxonomy_filter_refseq Filter RefSeq by taxonomy +taxonomy_krona_chart Krona pie chart from taxonomic profile +telescope Single locus resolution of Transposable ELEment expression. +tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. +transit TRANSIT +trycycler Trycycler toolkit wrappers +tsebra This tool has been developed to combine BRAKER predictions. +unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. +velvet de novo genomic assembler specially designed for short read sequencing technologies +velvet_optimiser Automatically optimize Velvet assemblies +verkko Telomere-to-telomere assembly pipeline +vigiechiro Tools created by the vigiechiro team to analyses and identify chiro sounds files. +wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. +xarray xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. +yahs Yet Another Hi-C scaffolding tool +zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. diff --git a/communities/genome/resources/tools.tsv b/communities/genome/resources/tools.tsv deleted file mode 100644 index 890b393f..00000000 --- a/communities/genome/resources/tools.tsv +++ /dev/null @@ -1,1476 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq 2022-05-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 307 307 80 80 8 8 3 3 3 3 1 1 318 318 84 84 False -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 False -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source 2015-11-17 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 474 2914 132 163 0 0 0 0 0 0 0 0 474 2914 132 163 False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 False -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 False -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq 2021-10-08 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49465 49465 281 281 0 0 0 0 0 0 0 0 49465 49465 281 281 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 False -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -add_input_name_as_column addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column 2020-03-24 mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 76834 86002 227 246 20174 20953 312 395 11 11 2 2 97019 106966 541 643 False -add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file 2020-11-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 15933 15933 378 378 1736 1736 214 214 380 380 28 28 18049 18049 620 620 False -add_value addValue Add a value as a new column. To update Text Manipulation add_value 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 37860 374587 1293 1610 17588 293713 1243 6197 3873 4397 202 229 59321 672697 2738 8036 False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro 2017-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 False -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 False -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 False -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 False -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services 2020-06-29 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 3600 3760 883 911 6 6 4 4 0 0 0 0 3606 3766 887 915 False -appendfdr append_fdr To update appendfdr 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 False -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning 2020-10-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 False -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services 2017-08-11 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 False -astropytools astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations To update https://github.com/astropy/astropy Astronomy astropytools 2023-04-11 volodymyrss https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0.1.0+galaxy0 astropy 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 5 5 0 0 0 0 0 0 0 0 13 13 5 5 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 False -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx 2015-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 131 15 20 329 785 50 210 0 0 0 0 412 916 65 230 False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 False -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 False -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 False -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 False -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 False -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source 2022-03-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 False -basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 226 308 27 35 2615 45557 302 2284 482 522 32 36 3323 46387 361 2355 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil 2019-05-22 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 306 311 82 83 467 467 99 99 0 0 0 0 773 778 181 182 False -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers batched_lastz 2024-04-30 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 5 5 0 0 0 0 123 123 5 5 False -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 False -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 False -bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://www.encodeproject.org/software/bedgraphtobigwig/ Convert Formats bbgbigwig 2024-06-14 iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig 0.1 ucsc-bedgraphtobigwig 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 7 7 175 175 26 26 0 0 0 0 217 217 33 33 False -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 False -bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.21 Data handling, Variant calling DNA polymorphism, GWAS study, Genotyping experiment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 False -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 2023-08-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 33 33 9 9 0 0 0 0 0 0 0 0 33 33 9 9 False -beacon2-import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://pypi.org/project/beacon2-import/ Variant Analysis Beacon2_Import 2024-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import 2.2.4 beacon2-import 2.2.4 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 12 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 7 7 0 0 0 0 0 0 0 0 22 22 7 7 False -beagle beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle 2021-07-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 28 28 0 0 0 0 0 0 0 0 88 88 28 28 False -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 False -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed 2023-08-08 iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 36 36 181 181 62 62 0 0 0 0 274 274 98 98 False -bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 Mapping Genomics 37 37 37 37 37 37 37 37 0 0 0 0 0 0 0 0 37 6 37 0 0 37 0 0 0 37 0 0 0 0 0 0 37 37 37 0 916111 962278 13235 14525 407944 647621 25849 41751 84008 89233 2486 2832 1408063 1699132 41570 59108 False -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 False -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 False -bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph 2015-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph 2021-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 469 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig 2018-09-25 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 469 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers 2018-04-23 iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.9 python-bioext 0.21.9 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 17413 17413 822 822 15349 15349 2020 2020 2 2 1 1 32764 32764 2843 2843 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter 2019-03-15 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 False -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 False -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast 2022-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 738 738 151 151 0 0 0 0 2 2 1 1 740 740 152 152 False -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 False -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 False -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 False -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 False -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 False -bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 2018-04-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 Read mapping Mapping, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 397893 427447 12133 13176 577209 903193 33086 52020 60105 67495 3779 4271 1035207 1398135 48998 69467 False -bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 24164 25149 1320 1480 17537 203397 1330 17491 15654 15992 291 351 57355 244538 2941 19322 False -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -breseq breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq 2019-10-21 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.39.0 Polymorphism detection Sequencing, Sequence analysis, DNA mutation 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 2976 2976 98 98 0 0 0 0 884 884 70 70 3860 3860 168 168 False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 False -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 False -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 False -bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa 2017-11-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 2 976935 1017671 13526 14401 474702 681286 32627 47624 79802 87191 4219 4954 1531439 1786148 50372 66979 False -bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 2021-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 Sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 56619 56619 2324 2324 36631 36631 2808 2808 18121 18121 713 713 111371 111371 5845 5845 False -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 False -c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s 2021-04-13 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.3.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 234 234 11 11 4 4 4 4 92 92 3 3 330 330 18 18 False -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 False -cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads 2021-06-19 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 1 1 0 0 0 0 0 0 0 0 52 52 1 1 False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param 2021-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1393 1393 10 10 0 0 0 0 0 0 0 0 1393 1393 10 10 False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu 2018-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 De-novo assembly Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13360 14618 1383 1444 0 0 0 0 3542 3542 385 385 16902 18160 1768 1829 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 175 28 39 0 0 0 0 0 0 0 0 88 175 28 39 False -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis 2021-09-01 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 218 218 17 17 0 0 0 0 0 0 0 0 218 218 17 17 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm 2021-06-15 climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 2 2 0 0 0 0 0 0 0 0 14 14 2 2 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services 2018-11-05 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -change_case ChangeCase Convert column case. To update Text Manipulation change_case 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 10606 12531 2204 2547 9044 17167 1748 2394 923 938 240 245 20573 30636 4192 5186 False -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 False -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca 2024-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.10 0 0 8 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 727 727 76 76 0 0 0 0 0 0 0 0 727 727 76 76 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 False -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 False -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos 2020-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 Sequence visualisation 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 26265 26265 2483 2483 31332 31332 3535 3535 26359 26359 999 999 83956 83956 7017 7017 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 False -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 False -cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 513 813 18 35 2406 30579 156 1547 1353 1393 17 20 4272 32785 191 1602 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 False -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 False -cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.1.0 cnv-vcf2json 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit 2023-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 Variant calling 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 618 618 177 177 0 0 0 0 0 0 0 0 618 618 177 177 False -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 False -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 False -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 False -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 False -collection_column_join collection_column_join Column Join on Collections To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join Text Manipulation collection_column_join 2016-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 23979 25337 3827 4011 21671 25163 4645 5045 2939 3036 688 701 48589 53536 9160 9757 False -collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers Text Manipulation collection_element_identifiers 2018-06-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6905 7102 1620 1630 7761 7761 1897 1897 1157 1157 243 243 15823 16020 3760 3770 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -column_arrange_by_header bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header 2015-03-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5356 5636 446 484 2026 2026 375 375 1400 1531 117 138 8782 9193 938 997 False -column_maker Add_a_column1 Compute an expression on every row To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker Text Manipulation column_maker 2019-06-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2940752 3907183 5422 6121 263254 737503 6095 13728 96478 97667 884 974 3300484 4742353 12401 20823 False -column_order_header_sort column_order_header_sort Sort Column Order by heading To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort Text Manipulation column_order_header_sort 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3735 3891 268 297 1923 1923 381 381 0 0 0 0 5658 5814 649 678 False -column_remove_by_header column_remove_by_header Remove columns by header To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header Text Manipulation column_remove_by_header 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8331 8917 613 662 5206 5206 716 716 1976 1976 27 27 15513 16099 1356 1405 False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 False -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 False -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 False -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 False -complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 187 233 15 20 495 4810 165 836 405 451 7 7 1087 5494 187 863 False -compose_text_param compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param 2019-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 45827 45831 689 691 7721 7721 303 303 1481 1481 121 121 55029 55033 1113 1115 False -compress_file compress_file Compress files. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file Text Manipulation compress_file 2022-02-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6343 6343 290 290 3674 3674 286 286 11832 11832 59 59 21849 21849 635 635 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 575128 575441 694 783 43420 85345 629 3508 19330 19418 104 117 637878 680204 1427 4408 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets 2019-04-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 4822 4824 613 614 1317 1317 204 204 3088 3795 252 289 9227 9936 1069 1107 False -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired 2019-12-16 nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 False -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2173 28 368 195 205 8 8 242 2378 36 376 False -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 23589 28986 1061 1200 23507 160693 2302 8699 5413 6446 251 329 52509 196125 3614 10228 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler 2018-12-07 lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.21 4 0 5 0 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 170 170 26 26 195 195 39 39 0 0 0 0 365 365 65 65 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1560 1725 43 58 4328 44209 193 2113 283 316 16 18 6171 46250 252 2189 False -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 False -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 False -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 False -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies Up-to-date http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap 2017-07-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.7.0 crossmap 0.7.0 5 0 6 0 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 2182 2182 331 331 5251 5251 903 903 0 0 0 0 7433 7433 1234 1234 False -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 False -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 False -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk 2019-08-27 nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cta cta_astro_tool Basic simulation of CTA telescope observations using gammapy package To update Astronomy cta_astro_tool 2024-04-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0.0.1+galaxy0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 False -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 False -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 False -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 False -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 False -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 False -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 False -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 False -cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular 2014-12-22 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 1208 43 97 1334 2683 101 479 0 0 0 0 2222 3891 144 576 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1973168 2034965 11939 12833 352364 803522 12967 30199 128777 133584 2341 2572 2454309 2972071 27247 45604 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Up-to-date https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv 2020-09-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 2.1.1 cutesv 2.1.1 Split read mapping, Genotyping, Structural variation detection Sequencing, Computer science 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 260 260 43 43 0 0 0 0 119 119 8 8 379 379 51 51 False -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 173 280 41 83 0 0 0 0 173 280 41 83 False -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 False -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga 2016-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation 2015-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 1 3 3 0 0 1 0 0 0 1 0 0 0 0 0 0 3 3 3 0 748586 760943 7066 7307 98089 112831 5306 6131 16235 16317 2161 2171 862910 890091 14533 15609 False -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 False -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 False -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -deepvariant deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant 2021-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2561 2561 325 325 2916 2916 460 460 0 0 0 0 5477 5477 785 785 False -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 False -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 False -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly 2020-10-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.3.1 Indel detection, Structural variation detection, Genotyping Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 1451 1451 288 288 0 0 0 0 0 0 0 0 1451 1451 288 288 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator 2013-11-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 69 26 30 0 304 0 133 0 0 0 0 59 373 26 163 False -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 False -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 False -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 False -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 False -diff diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff 2020-03-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 362 362 99 99 23 23 17 17 0 0 0 0 385 385 116 116 False -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 False -diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq Up-to-date http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2018-04-07 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 3.12.0 bioconductor-diffbind 3.12.0 Differential binding analysis ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7092 7663 606 652 14367 18624 1360 1916 1477 1640 69 84 22936 27927 2035 2652 False -diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -digestdb digestdb To update digestdb 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -directag_and_tagrecon To update directag_and_tagrecon 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 False -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot 2022-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver 2022-12-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 False -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools 2016-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.1 six 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 406 133 163 1421 1421 547 547 0 0 0 0 1697 1827 680 710 False -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta 2022-10-16 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4495 4495 111 111 0 0 0 0 0 0 0 0 4495 4495 111 111 False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa 2022-11-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload 2020-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.3 ena-upload-cli 0.7.4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 366 366 41 41 0 0 0 0 1302 1302 14 14 1668 1668 55 55 False -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch 2017-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1989 2302 367 453 0 0 0 0 0 0 0 0 1989 2302 367 453 False -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 False -ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep 2022-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 112.0 ensembl-vep 113.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3051 3051 171 171 0 0 0 0 0 0 0 0 3051 3051 171 171 False -eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie 2021-12-30 climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 4 4 0 0 0 0 0 0 0 0 45 45 4 4 False -epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg 2018-03-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 160 252 17 21 0 0 0 0 0 0 0 0 160 252 17 21 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability 2019-05-03 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 336 39 40 0 0 0 0 0 0 0 0 232 336 39 40 False -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 False -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 False -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster 2016-01-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 False -extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna 2016-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 9409 12735 813 923 20180 259099 2072 11791 168 611 20 63 29757 272445 2905 12777 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 False -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 False -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 False -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates 2020-10-21 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 264 264 69 69 34 34 11 11 103 103 1 1 401 401 81 81 False -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf 2023-01-11 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 385 385 46 46 587 587 107 107 58 58 5 5 1030 1030 158 158 False -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 False -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 False -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 False -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko 2018-04-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6690 8818 554 612 0 0 0 0 0 0 0 0 6690 8818 554 612 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -find_subsequences bg_find_subsequences To update find_subsequences 2015-03-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 784 69 79 2820 3047 323 361 20 20 1 1 3394 3851 393 441 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 589 731 51 63 2445 32847 304 2549 1214 1294 15 22 4248 34872 370 2634 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -footprint footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint 2017-04-18 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 5 5 0 0 0 0 0 0 0 0 57 57 5 5 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 False -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 False -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Up-to-date https://github.com/ekg/freebayes Variant Analysis freebayes 2017-01-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.8 freebayes 1.3.8 Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 149715 171093 8158 8794 144708 256315 15996 25107 19156 21936 2251 2571 313579 449344 26405 36472 False -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec 2020-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk Copy number estimation, Variant calling, Genome alignment Oncology, Human genetics, Data mining 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 748 748 91 91 0 0 0 0 12 12 1 1 760 760 92 92 False -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 False -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox 2018-06-05 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 2019-07-31 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution 2019-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 578 578 34 34 0 0 0 0 578 578 34 34 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 2021-12-29 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 2019-10-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3463 3463 452 452 9040 9040 1639 1639 0 0 0 0 12503 12503 2091 2091 False -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp 2017-06-23 iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 False -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 False -genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta 2020-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 4 4 2 2 221 2905 23 279 0 0 0 0 225 2909 25 281 False -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 Variant Analysis genehunter_modscore 2017-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 False -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services 2023-04-07 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.16 genoboo 0.4.16 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 False -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 660 104 197 0 0 0 0 445 660 104 197 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 False -genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich 2019-07-05 iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3534 3577 402 405 2840 2840 419 419 571 571 31 31 6945 6988 852 855 False -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage 2018-06-13 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3768 325011 1462 2044 9350 242043 2201 6583 787 1070 119 146 13905 568124 3782 8773 False -get_hrun get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 False -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9664 9775 763 765 5623 5623 493 493 1000 1000 135 135 16287 16398 1391 1393 False -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 False -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 False -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 False -gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed 2018-01-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 2230 329 347 1071 1071 362 362 492 492 64 64 2938 3793 755 773 False -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 False -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset 2022-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 False -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 False -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 False -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali 2020-03-30 nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 False -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation 2018-04-24 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 377 400 17 17 0 0 0 0 0 0 0 0 377 400 17 17 False -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 False -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 False -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 2018-05-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8329 9363 3336 3828 8009 8009 3130 3130 1577 1577 344 344 17915 18949 6810 7302 False -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. To update https://github.com/sequencing/gvcftools Variant Analysis 2016-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 False -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy 2022-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 False -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 2018-07-22 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 False -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hess hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope To update Astronomy hess_astro_tool 2024-02-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0.0.2+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 False -hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard To update https://github.com/VariantEffect/hgvsParseR/tree/master Variant Analysis hgvsparser 2024-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6346 6346 2 2 0 0 0 0 0 0 0 0 6346 6346 2 2 False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 False -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk 2024-02-03 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 1.0.0 hictk 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 9 9 0 0 0 0 0 0 0 0 17 17 9 9 False -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup 2017-03-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 7 0 7 0 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 901 1020 160 184 440 440 111 111 0 0 0 0 1341 1460 271 295 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 False -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.8.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 False -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 False -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 False -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 False -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 False -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 False -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids 2020-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.45 omero-py 5.11.1 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 404 404 37 37 0 0 0 0 24 24 1 1 428 428 38 38 False -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 False -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 False -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 False -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 False -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 False -intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter To update https://github.com/intermine Convert Formats intermine_galaxy_exchange 2018-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 6 12 72 87 13 15 108 108 1 1 217 241 20 28 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 False -intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20472 349984 2351 3007 45587 778988 4359 14116 6087 7417 484 561 72146 1136389 7194 17684 False -interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf 2020-07-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.13.0 Sequence analysis 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 107 7 10 758 19538 87 1246 16 24 2 2 806 19669 96 1258 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 False -irissv irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.21 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 False -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -jasminesv jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 9 9 53 53 19 19 0 0 0 0 85 85 28 28 False -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 False -jbrowse jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container 2016-11-08 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 False -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15624 330820 1864 2438 52317 513688 10198 39421 1329 1645 213 289 69270 846153 12275 42148 False -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id Text Manipulation join_files_by_id 2017-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy 2017-11-26 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1980 2697 345 410 0 0 0 0 1081 1081 44 44 3061 3778 389 454 False -jq jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 660 2374 61 63 336 336 82 82 281 281 11 11 1277 2991 154 156 False -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff 2017-09-27 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip 2018-05-16 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit 2021-02-11 iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7179 7179 509 509 11138 11138 1145 1145 0 0 0 0 18317 18317 1654 1654 False -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 False -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 False -kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers kegalign 2024-08-29 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 0.1.2.7 kegalign-full 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 5 5 1 1 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -king king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king 2021-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 False -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.4.14 kma 1.4.15 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 False -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 False -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 False -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 False -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 False -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 False -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 False -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 False -lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz 2018-02-19 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 Sequence alignment, Read mapping Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 77409 84356 447 475 156658 193590 870 3511 38579 38780 173 203 272646 316726 1490 4189 False -lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 3 4 0 0 0 0 8 10 5 5 15 19 8 9 False -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 False -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie 2022-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 False -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis 2019-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 5 5 5 4 5 5 5 4 0 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4176367 4176367 4301 4301 509615 509615 8213 8213 106342 106342 1815 1815 4792324 4792324 14329 14329 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 False -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 False -ltq_iquant_cli To update ltq_iquant_cli 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove 2020-07-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv 2020-11-12 iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1534 1534 199 199 0 0 0 0 0 0 0 0 1534 1534 199 199 False -lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 1.3 lumpy-sv 0.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 False -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 False -maf_stats maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats 2020-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 15 21 7 9 227 2470 52 464 1 1 1 1 243 2492 60 474 False -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 False -maftoaxt maftoaxt Convert dataset from MAF to axt format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_maftoaxt 2024-07-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt 469 ucsc-maftoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing 2018-03-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 Genetic variation analysis Genetics, Genetic variation, Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 11761 12093 873 889 5762 5762 473 473 5610 5610 343 343 23133 23465 1689 1705 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 False -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 False -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run 2021-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 9 9 0 0 0 0 0 0 0 0 24 24 9 9 False -manta manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta 2023-06-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 218 218 34 34 0 0 0 0 0 0 0 0 218 218 34 34 False -map_param_value map_param_value Map a parameter value to another value To update Text Manipulation map_param_value 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3780 3780 67 67 1012 1012 57 57 105 105 3 3 4897 4897 127 127 False -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 False -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer 2023-12-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 0 0 0 0 0 0 0 0 8 8 2 2 False -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 False -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 False -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 743 816 103 141 292 2868 82 459 0 0 0 0 1035 3684 185 600 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 False -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme 2018-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.5.6 meme 5.5.7 Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability 3 0 4 0 3 0 4 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 20990 22979 762 892 10975 25929 1551 3249 0 0 0 0 31965 48908 2313 4141 False -meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip 2018-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6413 7000 705 743 7260 7260 1171 1171 0 0 0 0 13673 14260 1876 1914 False -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco 2018-06-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 565922 566630 418 441 45844 107523 671 4353 19828 19994 100 137 631594 694147 1189 4931 False -merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 20905 31051 1906 2128 21780 132833 885 3172 1524 1925 122 152 44209 165809 2913 5452 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin 2020-04-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 Haplotype mapping GWAS study, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 False -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 False -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 False -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 False -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 False -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 False -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 False -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 False -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit 2016-12-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -mgf_formatter mgf_formatter Up-to-date mgf_formatter 2014-09-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 False -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 False -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 False -mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 8 8 17 63 6 19 0 0 0 0 26 74 14 27 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 2018-08-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 Pairwise sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 346530 349075 4323 4419 108535 108535 4075 4075 22331 22331 1166 1166 477396 479941 9564 9660 False -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 False -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 False -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 False -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko 2018-04-12 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 False -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 False -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 False -moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs 2019-07-28 iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 339 339 56 56 0 0 0 0 0 0 0 0 339 339 56 56 False -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 False -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mosdepth mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth 2022-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1278 1278 87 87 168 168 24 24 102 102 5 5 1548 1548 116 116 False -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 False -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 False -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 False -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 False -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 False -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 False -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps 2017-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 485 871 159 298 0 0 0 0 485 871 159 298 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 False -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 False -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 False -mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 49 5 5 81 417 23 118 0 0 0 0 125 466 28 123 False -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns 2020-10-19 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 False -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 False -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish 2018-06-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 9284 9694 215 229 0 0 0 0 2358 2358 49 49 11642 12052 264 278 False -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 False -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 False -ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download 2019-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6873 6873 1664 1664 17651 17651 4513 4513 6228 6228 972 972 30752 30752 7149 7149 False -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 False -ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.20.0 ncbi-datasets-cli Data handling, Sequence database search, Data retrieval Biological databases 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4417 4417 1024 1024 6940 6940 2275 2275 1 1 1 1 11358 11358 3300 3300 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct 2022-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 22.4 entrez-direct 22.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 3 0 2 False -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils 2020-08-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 4 0 0 4 0 0 0 2 0 0 0 0 0 0 0 7 7 0 2794 3191 533 664 0 0 0 0 0 0 0 0 2794 3191 533 664 False -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 False -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr 2022-08-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 6 6 0 0 0 0 0 0 0 0 12 12 6 6 False -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 False -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr 2020-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1403 1403 49 49 0 0 0 0 0 0 0 0 1403 1403 49 49 False -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM 2015-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24611 29662 633 716 15523 21395 740 1128 7751 8972 125 145 47885 60029 1498 1989 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 False -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ococo ococo Variant detection of SNVs To update https://github.com/karel-brinda/ococo Variant Analysis ococo 2017-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1850 1963 79 93 1370 1370 194 194 0 0 0 0 3220 3333 273 287 False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit 2017-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 582 663 68 69 0 0 0 0 0 0 0 0 582 663 68 69 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 False -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 False -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe 2022-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 False -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader Data Source packaged_annotation_loader 2022-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 False -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp 2022-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 Variant calling Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 2022-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.14.99 pbmm2 1.14.99 Pairwise sequence alignment, Sorting Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 17 17 0 0 0 0 0 0 0 0 70 70 17 17 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram 2016-06-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.2 openjdk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5505 5505 510 510 7932 8582 811 909 736 736 119 119 14173 14823 1440 1538 False -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 False -peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla 2024-02-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 False -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 False -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 False -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 False -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 False -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 False -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools 2017-09-28 bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat 2022-01-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 109 109 29 29 250 250 84 84 0 0 0 0 359 359 113 113 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 False -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard 2019-05-30 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.3.0 Formatting Sequencing 31 31 31 31 31 31 31 31 0 0 0 0 0 0 0 0 31 4 31 0 0 31 0 0 0 31 0 0 0 0 0 0 31 31 31 0 386934 399039 11024 11956 366646 589980 32000 57111 56622 62258 2845 3398 810202 1051277 45869 72465 False -pick_value pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value 2023-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1607 1607 41 41 490 490 53 53 127 127 4 4 2224 2224 98 98 False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 False -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 False -pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval 2015-03-06 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 613 640 48 54 1381 7804 201 1552 756 815 22 30 2750 9259 271 1636 False -pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3639 3774 414 461 9754 52522 1247 4531 1893 2433 191 318 15286 58729 1852 5310 False -pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update https://github.com/broadinstitute/pilon/wiki Variant Analysis pilon 2016-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 Sequence assembly, Analysis Assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9045 9458 1115 1144 7989 7989 1070 1070 3945 4137 726 741 20979 21584 2911 2955 False -pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel 2021-09-29 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign 2019-08-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1245 1245 231 231 9046 9046 630 630 0 0 0 0 10291 10291 861 861 False -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 False -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 False -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 False -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink 2020-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 Genetic variation analysis GWAS study 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 851 851 127 127 249 249 43 43 0 0 0 0 1100 1100 170 170 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 False -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 False -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat 2020-03-24 nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment 2016-11-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment 2016-11-07 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 False -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 False -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 False -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 False -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 False -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 False -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 False -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 False -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 False -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 False -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 False -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 False -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 False -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 False -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 False -protxml_to_xls protxml_to_xls To update protxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_eval psm_eval To update psm_eval 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 False -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2716 2716 104 104 134 134 43 43 40 40 1 1 2890 2890 148 148 False -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 False -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -pyvo_integration astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy To update Data Source astronomicalarchivestool 2023-08-26 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0.10.0 astropy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 6 6 0 0 0 0 0 0 0 0 53 53 6 6 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 False -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 False -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 False -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 False -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 False -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 False -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -query query Execute an SQL statement on a set of tables To update Text Manipulation query 2020-12-09 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -query_impc query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc 2023-10-11 iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular Text Manipulation 2017-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.1 python 3 3 3 1 3 3 3 1 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 130124 135361 1265 1305 11135 11135 922 922 5939 5939 153 153 147198 152435 2340 2380 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 False -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 False -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 False -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 False -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 False -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 False -regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace 2017-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 78648 78834 1144 1156 18063 18063 870 870 4455 6051 194 289 101166 102948 2208 2315 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 148572 169964 3525 3682 36694 113826 3910 8163 9713 10577 1475 1598 194979 294367 8910 13443 False -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 False -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file 2017-02-24 bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 577184 577312 463 492 43900 44233 283 373 2190 2190 112 112 623274 623735 858 977 False -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names 2017-05-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 514 573 69 83 0 0 0 0 0 0 0 0 514 573 69 83 False -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 415 721 128 219 0 0 0 0 415 721 128 219 False -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3543 3619 108 111 536 536 157 157 0 0 0 0 4079 4155 265 268 False -resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window 2016-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 86 8 9 138 216 30 57 0 0 0 0 213 302 38 66 False -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam 2019-04-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.21 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 11 11 520 520 31 31 0 0 0 0 560 560 42 42 False -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 False -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 False -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 False -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 False -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 False -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 False -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 False -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 False -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor 2023-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths 2022-10-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign 2022-03-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba 2022-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools 2022-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser 2022-06-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps 2016-01-29 earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 False -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1155 1251 57 63 2264 18187 189 1748 525 590 10 17 3944 20028 256 1828 False -sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python 1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 278 12 26 3554 76029 450 6346 229 345 16 29 3879 76652 478 6401 False -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba 2020-05-19 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 684 684 17 17 684 684 17 17 False -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! Up-to-date https://github.com/biod/sambamba SAM sambamba 2016-06-23 bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 1.0.1 sambamba 1.0.1 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 297 297 51 51 0 0 0 0 0 0 0 0 297 297 51 51 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools To update https://github.com/samtools/samtools SAM 2021-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.20 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa 2020-12-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.2 sansa 0.2.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 138 138 36 36 0 0 0 0 0 0 0 0 138 138 36 36 False -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 False -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 False -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol 2022-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scaffold scaffold, scaffold_export To update scaffold 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 False -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -scripting singularity_scriptrunner suite_scripting To update https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ Text Manipulation scripting tools 2023-07-29 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr 2020-02-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5106 5106 116 116 6419 6419 241 241 0 0 0 0 11525 11525 357 357 False -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 281 2284 10 53 0 0 0 0 0 0 0 0 281 2284 10 53 False -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign 2024-04-18 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.7 segalign-galaxy 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 252 252 47 47 0 0 0 0 252 252 47 47 False -segemehl segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1095 1306 98 113 0 0 0 0 0 0 0 0 1095 1306 98 113 False -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 False -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 False -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 False -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 False -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 False -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sgwb sgwb_astro_tool SGWB To update Astronomy sgwb_astro_tool 2024-04-17 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0.0.1+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 0 0 0 0 0 0 0 0 5 5 2 2 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 64 4 4 0 0 0 0 0 0 0 0 54 64 4 4 False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 27232 36366 2184 2789 16648 84460 4191 18767 2785 3276 373 452 46665 124102 6748 22008 False -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1620 2660 378 589 10551 24579 682 1851 284 398 67 83 12455 27637 1127 2523 False -sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 276 379 30 42 972 9053 146 1008 644 689 5 7 1892 10121 181 1057 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext 2021-02-28 iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 0 2 4 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 220 220 68 68 0 0 0 0 416 416 10 10 636 636 78 78 False -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 False -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 False -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes 2019-04-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 False -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 False -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 False -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists 2019-10-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6555 6555 807 807 5336 5336 171 171 1143 1143 182 182 13034 13034 1160 1160 False -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites 2017-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6597 6597 663 663 1467 1467 256 256 1279 1279 114 114 9343 9343 1033 1033 False -snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff 2018-07-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 5 5 5 5 5 5 5 5 0 0 0 0 0 1 0 0 0 5 5 0 0 5 0 0 0 5 0 0 0 0 0 0 5 5 5 0 103826 108296 7181 7908 115727 178110 15871 22769 11817 13155 2148 2321 231370 299561 25200 32998 False -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 SNP detection DNA polymorphism, Nucleic acid sites, features and motifs 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 764895 764895 1276 1276 94572 94572 1636 1636 26990 26990 561 561 886457 886457 3473 3473 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region To update https://github.com/BrownfieldPlantLab/SNPFreqPlot Variant Analysis snpfreqplot 2020-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 3683 3683 338 338 1401 1401 433 433 1029 1029 95 95 6113 6113 866 866 False -snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift 2015-04-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 8 8 8 8 8 8 8 8 0 0 0 0 0 8 0 0 0 0 8 0 0 8 0 0 0 8 0 0 0 0 0 0 8 8 8 0 5142904 5146618 3602 4283 382391 421190 7013 9678 104030 105024 960 1184 5629325 5672832 11575 15145 False -snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 52 55 23 24 421 421 75 75 0 0 0 0 473 476 98 99 False -snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 509 554 107 128 474 474 190 190 0 0 0 0 983 1028 297 318 False -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv 2021-03-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 False -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_file_on_column tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5995 6261 408 453 2150 2150 311 311 26 26 2 2 8171 8437 721 766 False -split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection 2019-08-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16415 16623 968 984 9133 9133 672 672 4140 4140 148 148 29688 29896 1788 1804 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta 2015-10-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1772 1811 278 294 3012 3012 564 564 0 0 0 0 4784 4823 842 858 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 False -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 False -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 False -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 False -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign 2022-10-02 iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka 2021-01-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 669 669 112 112 1261 1261 417 417 0 0 0 0 1930 1930 529 529 False -stress_ng stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng 2021-03-04 bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 3 3 0 0 0 0 0 0 0 0 62 62 3 3 False -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 False -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 False -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 False -subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 566512 567199 410 470 49985 184650 1473 7631 20648 20897 155 188 637145 772746 2038 8289 False -subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1178 1450 124 141 3169 40539 636 3435 799 950 26 38 5146 42939 786 3614 False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 False -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 False -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib 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qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 False -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 False -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 False -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 False -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 False -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 False -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 False -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 False -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 False -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink 2017-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 False -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 False -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar 2013-12-02 devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16526 64515 2803 7456 0 0 0 0 16526 64515 2803 7456 False -table_compute table_compute Perform general-purpose table operations To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute Text Manipulation table_compute 2019-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 216072 216115 1811 1814 12326 12326 1558 1558 16136 16136 256 256 244534 244577 3625 3628 False -tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2188 2220 33 38 0 0 0 0 0 0 0 0 2188 2220 33 38 False -tabular_to_fasta tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 329032 333057 1489 1702 79033 215770 2441 8587 27876 33727 296 360 435941 582554 4226 10649 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 False -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 False -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 False -tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter 2019-10-03 iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22977 22977 461 461 3888 3888 274 274 3611 3611 80 80 30476 30476 815 815 False -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 False -tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.1 tbvcfreport 1.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2955 2955 335 335 6090 6090 348 348 2347 2347 72 72 11392 11392 755 755 False -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 False -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 False -text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing 2019-01-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 20 20 20 20 20 20 20 20 0 0 0 0 0 0 0 0 19 1 19 0 0 19 0 0 0 20 0 0 0 0 0 0 19 19 19 0 3898014 4015573 37698 42095 648268 915282 47636 69828 103365 105214 7778 7953 4649647 5036069 93112 119876 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 False -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 False -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 False -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 False -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 False -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 False -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update 2021-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.8 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 3314 3314 124 124 0 0 0 0 0 0 0 0 3314 3314 124 124 False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 False -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 False -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 False -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler 2019-04-15 nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmer trimmer Trim leading or trailing characters. To update Text Manipulation trimmer 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 5304 7438 447 512 15698 108672 658 2946 266 822 53 81 21268 116932 1158 3539 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 False -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services 2018-06-20 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 255 379 31 37 281 281 64 64 0 0 0 0 536 660 95 101 False -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa 2016-08-19 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 469 ucsc-twobittofa 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 413 511 84 118 441 441 123 123 21 21 2 2 875 973 209 243 False -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 False -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 False -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_axttomaf 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf 469 ucsc-axttomaf 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 False -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_nettoaxt 2024-09-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt 469 ucsc-nettoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 False -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 False -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 False -unzip unzip Unzip file To update https://github.com/bmcv Convert Formats unzip 2019-08-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 6.0 unzip 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6942 7024 1345 1356 1 1 1 1 2461 2461 266 266 9404 9486 1612 1623 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 False -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 False -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java 2020-08-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 381 381 37 37 0 0 0 0 0 0 0 0 381 381 37 37 False -variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer 2019-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 95 95 14 14 516 516 67 67 0 0 0 0 611 611 81 81 False -varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan 2018-11-29 iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 10711 11502 1442 1560 16705 16705 3135 3135 1036 1036 100 100 28452 29243 4677 4795 False -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf 2022-11-28 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 2013-11-17 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5058 6139 606 699 17232 53268 2965 5686 2298 2656 424 482 24588 62063 3995 6867 False -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 False -vcf2maf vcf2maf vcf2maf: Convert VCF into MAF To update https://github.com/mskcc/vcf2maf Convert Formats vcf2maf 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1097 1097 46 46 0 0 0 0 65 65 5 5 1162 1162 51 51 False -vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 221 57 65 1399 2700 209 584 0 0 0 0 1590 2921 266 649 False -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 169090 169679 823 874 16304 42215 1141 2594 2485 2511 169 172 187879 214405 2133 3640 False -vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 263 340 31 54 263 342 31 56 False -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 513 569 6 9 513 569 6 9 False -vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 400 455 129 140 0 0 0 0 238 606 19 56 638 1061 148 196 False -vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 3 0 0 0 0 335 463 19 28 335 482 19 31 False -vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 882 888 30 32 6118 8261 36 114 175 184 6 6 7175 9333 72 152 False -vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6879 17157 897 1219 7585 14509 1245 1925 1648 1681 225 229 16112 33347 2367 3373 False -vcfanno vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 SNP annotation Genetic variation, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1139 1139 174 174 0 0 0 0 0 0 0 0 1139 1139 174 174 False -vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2797 2850 157 181 3668 14532 652 1392 494 507 61 63 6959 17889 870 1636 False -vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 203 62 66 497 1828 155 387 184 197 11 11 870 2228 228 464 False -vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3017 4049 185 210 4709 20250 406 1147 507 527 40 42 8233 24826 631 1399 False -vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 416 478 35 40 3969 10457 82 309 362 378 8 8 4747 11313 125 357 False -vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 767 96 106 803 1895 222 627 241 256 16 17 1789 2918 334 750 False -vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1422 2020 284 505 4951 19530 1021 2669 493 516 60 62 6866 22066 1365 3236 False -vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 233 253 37 42 234 1839 79 287 199 214 11 12 666 2306 127 341 False -vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 572 585 90 92 2063 2427 139 296 272 290 19 22 2907 3302 248 410 False -vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37489 47142 2113 2218 75128 162296 5730 10533 2626 2736 320 331 115243 212174 8163 13082 False -vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 926 957 155 173 2291 5323 313 985 251 265 28 31 3468 6545 496 1189 False -vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 172 183 21 25 351 879 67 201 312 342 15 16 835 1404 103 242 False -vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 778 794 107 112 2414 3721 179 508 209 225 20 21 3401 4740 306 641 False -vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 502 555 134 143 3428 6338 266 858 220 235 23 24 4150 7128 423 1025 False -vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1964 1991 182 186 1937 3846 188 644 567 601 26 27 4468 6438 396 857 False -vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 269 310 38 42 358 1071 89 287 179 213 12 14 806 1594 139 343 False -vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 711 28 33 403 831 75 200 190 214 10 12 1183 1756 113 245 False -vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 168 13 15 153 350 27 75 184 192 6 6 498 710 46 96 False -vcfselectsamples vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 830 900 69 88 1315 6257 237 959 344 363 20 21 2489 7520 326 1068 False -vcfsort vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1868 1904 174 185 18378 24175 422 1279 537 674 70 73 20783 26753 666 1537 False -vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 192 81 90 1853 3943 581 1280 144 156 13 16 2152 4291 675 1386 False -vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 440 594 127 142 0 0 0 0 0 16 0 12 440 610 127 154 False -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus 2016-10-16 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcftools_isec vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 537 104 118 0 1 0 1 39 496 28 48 418 1034 132 167 False -vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 817 1084 244 273 0 0 0 0 93 448 44 60 910 1532 288 333 False -vcftools_slice vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 423 56 60 6261 8115 133 362 127 157 10 19 6798 8695 199 441 False -vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 142 46 49 0 0 0 0 120 142 12 19 254 284 58 68 False -vcfvcfintersect vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 976544 977015 703 748 64155 81830 981 2103 11044 11069 225 229 1051743 1069914 1909 3080 False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 False -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 False -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 False -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -weblogo3 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 2017-11-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2720 2818 206 228 10299 30578 1354 3657 1226 1285 50 59 14245 34681 1610 3944 False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 False -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig 2024-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 469 ucsc-wigtobigwig 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1601 1601 106 106 1108 1108 172 172 200 200 15 15 2909 2909 293 293 False -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 False -winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap 2021-04-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 279 279 46 46 12 12 4 4 0 0 0 0 291 291 50 50 False -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 False -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 False -xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet 2021-10-18 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 17 17 0 0 0 0 0 0 0 0 59 59 17 17 False -xpath xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 235 7 8 0 1 0 1 0 0 0 0 128 236 7 9 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 False -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 False -zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 96 9 12 0 0 0 0 0 0 0 0 83 96 9 12 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False diff --git a/communities/genome/resources/tools_filtered_by_ts_categories.json b/communities/genome/resources/tools_filtered_by_ts_categories.json new file mode 100644 index 00000000..cf3a7182 --- /dev/null +++ b/communities/genome/resources/tools_filtered_by_ts_categories.json @@ -0,0 +1,132946 @@ +[ + { + "Galaxy wrapper id": "askor", + "Galaxy tool ids": [ + "askor_de" + ], + "Description": "AskoR links EdgeR and AskOmics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/askomics/askoR", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "askor_de", + "Date of first commit of the suite": "2018-04-09", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", + "Galaxy wrapper version": "0.2", + "Conda id": "bioconductor-limma", + "Conda version": "3.58.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0, + "Tools available on Viral Variant Visualizer (VVV)": 0, + "No. of tool users (5 years) (usegalaxy.eu)": 0, + "No. of tool users (all time) (usegalaxy.eu)": 0, + "Tool usage (5 years) (usegalaxy.eu)": 0, + "Tool usage (all time) (usegalaxy.eu)": 0, + "No. of tool users (5 years) (usegalaxy.org)": 0, + "No. of tool users (all time) (usegalaxy.org)": 0, + "Tool usage (5 years) (usegalaxy.org)": 0, + "Tool usage (all time) (usegalaxy.org)": 0, + "No. of tool users (5 years) (usegalaxy.org.au)": 0, + "No. of tool users (all time) (usegalaxy.org.au)": 0, + "Tool usage (5 years) (usegalaxy.org.au)": 0, + "Tool usage (all time) (usegalaxy.org.au)": 0, + "No. of tool users (5 years) - 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq 2022-05-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 307 307 80 80 8 8 3 3 3 3 1 1 318 318 84 84 False -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 False -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source 2015-11-17 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 474 2914 132 163 0 0 0 0 0 0 0 0 474 2914 132 163 False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 False -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 False -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq 2021-10-08 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49465 49465 281 281 0 0 0 0 0 0 0 0 49465 49465 281 281 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 False -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -add_input_name_as_column addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column 2020-03-24 mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 76834 86002 227 246 20174 20953 312 395 11 11 2 2 97019 106966 541 643 False -add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file 2020-11-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 15933 15933 378 378 1736 1736 214 214 380 380 28 28 18049 18049 620 620 False -add_value addValue Add a value as a new column. To update Text Manipulation add_value 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 37860 374587 1293 1610 17588 293713 1243 6197 3873 4397 202 229 59321 672697 2738 8036 False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro 2017-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 False -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 False -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 False -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 False -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services 2020-06-29 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 3600 3760 883 911 6 6 4 4 0 0 0 0 3606 3766 887 915 False -appendfdr append_fdr To update appendfdr 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 False -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning 2020-10-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 False -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services 2017-08-11 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 False -astropytools astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations To update https://github.com/astropy/astropy Astronomy astropytools 2023-04-11 volodymyrss https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0.1.0+galaxy0 astropy 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 5 5 0 0 0 0 0 0 0 0 13 13 5 5 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 False -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx 2015-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 131 15 20 329 785 50 210 0 0 0 0 412 916 65 230 False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 False -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 False -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 False -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 False -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 False -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source 2022-03-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 False -basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 226 308 27 35 2615 45557 302 2284 482 522 32 36 3323 46387 361 2355 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil 2019-05-22 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 306 311 82 83 467 467 99 99 0 0 0 0 773 778 181 182 False -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers batched_lastz 2024-04-30 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 5 5 0 0 0 0 123 123 5 5 False -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 False -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 False -bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://www.encodeproject.org/software/bedgraphtobigwig/ Convert Formats bbgbigwig 2024-06-14 iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig 0.1 ucsc-bedgraphtobigwig 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 7 7 175 175 26 26 0 0 0 0 217 217 33 33 False -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 False -bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.21 Data handling, Variant calling DNA polymorphism, GWAS study, Genotyping experiment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 False -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 2023-08-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 33 33 9 9 0 0 0 0 0 0 0 0 33 33 9 9 False -beacon2-import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://pypi.org/project/beacon2-import/ Variant Analysis Beacon2_Import 2024-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import 2.2.4 beacon2-import 2.2.4 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 12 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 7 7 0 0 0 0 0 0 0 0 22 22 7 7 False -beagle beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle 2021-07-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 28 28 0 0 0 0 0 0 0 0 88 88 28 28 False -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 False -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed 2023-08-08 iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 36 36 181 181 62 62 0 0 0 0 274 274 98 98 False -bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 Mapping Genomics 37 37 37 37 37 37 37 37 0 0 0 0 0 0 0 0 37 6 37 0 0 37 0 0 0 37 0 0 0 0 0 0 37 37 37 0 916111 962278 13235 14525 407944 647621 25849 41751 84008 89233 2486 2832 1408063 1699132 41570 59108 False -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 False -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 False -bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph 2015-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph 2021-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 469 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig 2018-09-25 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 469 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers 2018-04-23 iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.9 python-bioext 0.21.9 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 17413 17413 822 822 15349 15349 2020 2020 2 2 1 1 32764 32764 2843 2843 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter 2019-03-15 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 False -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 False -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast 2022-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 738 738 151 151 0 0 0 0 2 2 1 1 740 740 152 152 False -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 False -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 False -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 False -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 False -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 False -bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 2018-04-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 Read mapping Mapping, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 397893 427447 12133 13176 577209 903193 33086 52020 60105 67495 3779 4271 1035207 1398135 48998 69467 False -bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 24164 25149 1320 1480 17537 203397 1330 17491 15654 15992 291 351 57355 244538 2941 19322 False -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -breseq breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq 2019-10-21 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.39.0 Polymorphism detection Sequencing, Sequence analysis, DNA mutation 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 2976 2976 98 98 0 0 0 0 884 884 70 70 3860 3860 168 168 False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 False -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 False -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 False -bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa 2017-11-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 2 976935 1017671 13526 14401 474702 681286 32627 47624 79802 87191 4219 4954 1531439 1786148 50372 66979 False -bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 2021-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 Sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 56619 56619 2324 2324 36631 36631 2808 2808 18121 18121 713 713 111371 111371 5845 5845 False -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 False -c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s 2021-04-13 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.3.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 234 234 11 11 4 4 4 4 92 92 3 3 330 330 18 18 False -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 False -cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads 2021-06-19 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 1 1 0 0 0 0 0 0 0 0 52 52 1 1 False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param 2021-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1393 1393 10 10 0 0 0 0 0 0 0 0 1393 1393 10 10 False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu 2018-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 De-novo assembly Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13360 14618 1383 1444 0 0 0 0 3542 3542 385 385 16902 18160 1768 1829 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 175 28 39 0 0 0 0 0 0 0 0 88 175 28 39 False -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis 2021-09-01 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 218 218 17 17 0 0 0 0 0 0 0 0 218 218 17 17 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm 2021-06-15 climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 2 2 0 0 0 0 0 0 0 0 14 14 2 2 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services 2018-11-05 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -change_case ChangeCase Convert column case. To update Text Manipulation change_case 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 10606 12531 2204 2547 9044 17167 1748 2394 923 938 240 245 20573 30636 4192 5186 False -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 False -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca 2024-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.10 0 0 8 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 727 727 76 76 0 0 0 0 0 0 0 0 727 727 76 76 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 False -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 False -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos 2020-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 Sequence visualisation 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 26265 26265 2483 2483 31332 31332 3535 3535 26359 26359 999 999 83956 83956 7017 7017 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 False -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 False -cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 513 813 18 35 2406 30579 156 1547 1353 1393 17 20 4272 32785 191 1602 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 False -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 False -cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.1.0 cnv-vcf2json 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit 2023-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 Variant calling 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 618 618 177 177 0 0 0 0 0 0 0 0 618 618 177 177 False -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 False -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 False -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 False -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 False -collection_column_join collection_column_join Column Join on Collections To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join Text Manipulation collection_column_join 2016-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 23979 25337 3827 4011 21671 25163 4645 5045 2939 3036 688 701 48589 53536 9160 9757 False -collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers Text Manipulation collection_element_identifiers 2018-06-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6905 7102 1620 1630 7761 7761 1897 1897 1157 1157 243 243 15823 16020 3760 3770 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -column_arrange_by_header bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header 2015-03-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5356 5636 446 484 2026 2026 375 375 1400 1531 117 138 8782 9193 938 997 False -column_maker Add_a_column1 Compute an expression on every row To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker Text Manipulation column_maker 2019-06-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2940752 3907183 5422 6121 263254 737503 6095 13728 96478 97667 884 974 3300484 4742353 12401 20823 False -column_order_header_sort column_order_header_sort Sort Column Order by heading To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort Text Manipulation column_order_header_sort 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3735 3891 268 297 1923 1923 381 381 0 0 0 0 5658 5814 649 678 False -column_remove_by_header column_remove_by_header Remove columns by header To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header Text Manipulation column_remove_by_header 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8331 8917 613 662 5206 5206 716 716 1976 1976 27 27 15513 16099 1356 1405 False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 False -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 False -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 False -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 False -complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 187 233 15 20 495 4810 165 836 405 451 7 7 1087 5494 187 863 False -compose_text_param compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param 2019-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 45827 45831 689 691 7721 7721 303 303 1481 1481 121 121 55029 55033 1113 1115 False -compress_file compress_file Compress files. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file Text Manipulation compress_file 2022-02-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6343 6343 290 290 3674 3674 286 286 11832 11832 59 59 21849 21849 635 635 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 575128 575441 694 783 43420 85345 629 3508 19330 19418 104 117 637878 680204 1427 4408 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets 2019-04-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 4822 4824 613 614 1317 1317 204 204 3088 3795 252 289 9227 9936 1069 1107 False -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired 2019-12-16 nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 False -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2173 28 368 195 205 8 8 242 2378 36 376 False -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 23589 28986 1061 1200 23507 160693 2302 8699 5413 6446 251 329 52509 196125 3614 10228 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler 2018-12-07 lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.21 4 0 5 0 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 170 170 26 26 195 195 39 39 0 0 0 0 365 365 65 65 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1560 1725 43 58 4328 44209 193 2113 283 316 16 18 6171 46250 252 2189 False -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 False -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 False -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 False -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies Up-to-date http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap 2017-07-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.7.0 crossmap 0.7.0 5 0 6 0 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 2182 2182 331 331 5251 5251 903 903 0 0 0 0 7433 7433 1234 1234 False -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 False -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 False -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk 2019-08-27 nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cta cta_astro_tool Basic simulation of CTA telescope observations using gammapy package To update Astronomy cta_astro_tool 2024-04-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0.0.1+galaxy0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 False -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 False -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 False -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 False -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 False -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 False -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 False -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 False -cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular 2014-12-22 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 1208 43 97 1334 2683 101 479 0 0 0 0 2222 3891 144 576 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1973168 2034965 11939 12833 352364 803522 12967 30199 128777 133584 2341 2572 2454309 2972071 27247 45604 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Up-to-date https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv 2020-09-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 2.1.1 cutesv 2.1.1 Split read mapping, Genotyping, Structural variation detection Sequencing, Computer science 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 260 260 43 43 0 0 0 0 119 119 8 8 379 379 51 51 False -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 173 280 41 83 0 0 0 0 173 280 41 83 False -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 False -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga 2016-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation 2015-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 1 3 3 0 0 1 0 0 0 1 0 0 0 0 0 0 3 3 3 0 748586 760943 7066 7307 98089 112831 5306 6131 16235 16317 2161 2171 862910 890091 14533 15609 False -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 False -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 False -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -deepvariant deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant 2021-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2561 2561 325 325 2916 2916 460 460 0 0 0 0 5477 5477 785 785 False -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 False -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 False -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly 2020-10-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.3.1 Indel detection, Structural variation detection, Genotyping Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 1451 1451 288 288 0 0 0 0 0 0 0 0 1451 1451 288 288 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator 2013-11-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 69 26 30 0 304 0 133 0 0 0 0 59 373 26 163 False -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 False -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 False -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 False -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 False -diff diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff 2020-03-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 362 362 99 99 23 23 17 17 0 0 0 0 385 385 116 116 False -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 False -diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq Up-to-date http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2018-04-07 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 3.12.0 bioconductor-diffbind 3.12.0 Differential binding analysis ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7092 7663 606 652 14367 18624 1360 1916 1477 1640 69 84 22936 27927 2035 2652 False -diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -digestdb digestdb To update digestdb 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -directag_and_tagrecon To update directag_and_tagrecon 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 False -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot 2022-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver 2022-12-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 False -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools 2016-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.1 six 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 406 133 163 1421 1421 547 547 0 0 0 0 1697 1827 680 710 False -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta 2022-10-16 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4495 4495 111 111 0 0 0 0 0 0 0 0 4495 4495 111 111 False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa 2022-11-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload 2020-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.3 ena-upload-cli 0.7.4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 366 366 41 41 0 0 0 0 1302 1302 14 14 1668 1668 55 55 False -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch 2017-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1989 2302 367 453 0 0 0 0 0 0 0 0 1989 2302 367 453 False -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 False -ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep 2022-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 112.0 ensembl-vep 113.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3051 3051 171 171 0 0 0 0 0 0 0 0 3051 3051 171 171 False -eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie 2021-12-30 climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 4 4 0 0 0 0 0 0 0 0 45 45 4 4 False -epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg 2018-03-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 160 252 17 21 0 0 0 0 0 0 0 0 160 252 17 21 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability 2019-05-03 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 336 39 40 0 0 0 0 0 0 0 0 232 336 39 40 False -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 False -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 False -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster 2016-01-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 False -extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna 2016-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 9409 12735 813 923 20180 259099 2072 11791 168 611 20 63 29757 272445 2905 12777 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 False -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 False -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 False -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates 2020-10-21 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 264 264 69 69 34 34 11 11 103 103 1 1 401 401 81 81 False -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf 2023-01-11 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 385 385 46 46 587 587 107 107 58 58 5 5 1030 1030 158 158 False -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 False -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 False -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 False -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko 2018-04-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6690 8818 554 612 0 0 0 0 0 0 0 0 6690 8818 554 612 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -find_subsequences bg_find_subsequences To update find_subsequences 2015-03-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 784 69 79 2820 3047 323 361 20 20 1 1 3394 3851 393 441 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 589 731 51 63 2445 32847 304 2549 1214 1294 15 22 4248 34872 370 2634 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -footprint footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint 2017-04-18 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 5 5 0 0 0 0 0 0 0 0 57 57 5 5 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 False -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 False -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Up-to-date https://github.com/ekg/freebayes Variant Analysis freebayes 2017-01-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.8 freebayes 1.3.8 Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 149715 171093 8158 8794 144708 256315 15996 25107 19156 21936 2251 2571 313579 449344 26405 36472 False -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec 2020-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk Copy number estimation, Variant calling, Genome alignment Oncology, Human genetics, Data mining 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 748 748 91 91 0 0 0 0 12 12 1 1 760 760 92 92 False -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 False -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox 2018-06-05 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 2019-07-31 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution 2019-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 578 578 34 34 0 0 0 0 578 578 34 34 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 2021-12-29 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 2019-10-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3463 3463 452 452 9040 9040 1639 1639 0 0 0 0 12503 12503 2091 2091 False -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp 2017-06-23 iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 False -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 False -genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta 2020-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 4 4 2 2 221 2905 23 279 0 0 0 0 225 2909 25 281 False -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 Variant Analysis genehunter_modscore 2017-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 False -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services 2023-04-07 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.16 genoboo 0.4.16 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 False -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 660 104 197 0 0 0 0 445 660 104 197 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 False -genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich 2019-07-05 iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3534 3577 402 405 2840 2840 419 419 571 571 31 31 6945 6988 852 855 False -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage 2018-06-13 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3768 325011 1462 2044 9350 242043 2201 6583 787 1070 119 146 13905 568124 3782 8773 False -get_hrun get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 False -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9664 9775 763 765 5623 5623 493 493 1000 1000 135 135 16287 16398 1391 1393 False -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 False -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 False -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 False -gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed 2018-01-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 2230 329 347 1071 1071 362 362 492 492 64 64 2938 3793 755 773 False -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 False -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset 2022-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 False -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 False -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 False -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali 2020-03-30 nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 False -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation 2018-04-24 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 377 400 17 17 0 0 0 0 0 0 0 0 377 400 17 17 False -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 False -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 False -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 2018-05-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8329 9363 3336 3828 8009 8009 3130 3130 1577 1577 344 344 17915 18949 6810 7302 False -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. To update https://github.com/sequencing/gvcftools Variant Analysis 2016-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 False -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy 2022-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 False -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 2018-07-22 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 False -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hess hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope To update Astronomy hess_astro_tool 2024-02-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0.0.2+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 False -hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard To update https://github.com/VariantEffect/hgvsParseR/tree/master Variant Analysis hgvsparser 2024-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6346 6346 2 2 0 0 0 0 0 0 0 0 6346 6346 2 2 False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 False -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk 2024-02-03 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 1.0.0 hictk 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 9 9 0 0 0 0 0 0 0 0 17 17 9 9 False -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup 2017-03-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 7 0 7 0 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 901 1020 160 184 440 440 111 111 0 0 0 0 1341 1460 271 295 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 False -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.8.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 False -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 False -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 False -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 False -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 False -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 False -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids 2020-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.45 omero-py 5.11.1 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 404 404 37 37 0 0 0 0 24 24 1 1 428 428 38 38 False -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 False -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 False -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 False -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 False -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 False -intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter To update https://github.com/intermine Convert Formats intermine_galaxy_exchange 2018-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 6 12 72 87 13 15 108 108 1 1 217 241 20 28 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 False -intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20472 349984 2351 3007 45587 778988 4359 14116 6087 7417 484 561 72146 1136389 7194 17684 False -interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf 2020-07-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.13.0 Sequence analysis 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 107 7 10 758 19538 87 1246 16 24 2 2 806 19669 96 1258 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 False -irissv irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.21 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 False -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -jasminesv jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 9 9 53 53 19 19 0 0 0 0 85 85 28 28 False -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 False -jbrowse jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container 2016-11-08 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 False -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15624 330820 1864 2438 52317 513688 10198 39421 1329 1645 213 289 69270 846153 12275 42148 False -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id Text Manipulation join_files_by_id 2017-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy 2017-11-26 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1980 2697 345 410 0 0 0 0 1081 1081 44 44 3061 3778 389 454 False -jq jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 660 2374 61 63 336 336 82 82 281 281 11 11 1277 2991 154 156 False -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff 2017-09-27 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip 2018-05-16 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit 2021-02-11 iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7179 7179 509 509 11138 11138 1145 1145 0 0 0 0 18317 18317 1654 1654 False -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 False -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 False -kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers kegalign 2024-08-29 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 0.1.2.7 kegalign-full 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 5 5 1 1 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -king king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king 2021-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 False -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.4.14 kma 1.4.15 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 False -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 False -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 False -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 False -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 False -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 False -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 False -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 False -lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz 2018-02-19 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 Sequence alignment, Read mapping Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 77409 84356 447 475 156658 193590 870 3511 38579 38780 173 203 272646 316726 1490 4189 False -lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 3 4 0 0 0 0 8 10 5 5 15 19 8 9 False -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 False -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie 2022-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 False -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis 2019-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 5 5 5 4 5 5 5 4 0 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4176367 4176367 4301 4301 509615 509615 8213 8213 106342 106342 1815 1815 4792324 4792324 14329 14329 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 False -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 False -ltq_iquant_cli To update ltq_iquant_cli 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove 2020-07-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv 2020-11-12 iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1534 1534 199 199 0 0 0 0 0 0 0 0 1534 1534 199 199 False -lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 1.3 lumpy-sv 0.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 False -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 False -maf_stats maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats 2020-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 15 21 7 9 227 2470 52 464 1 1 1 1 243 2492 60 474 False -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 False -maftoaxt maftoaxt Convert dataset from MAF to axt format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_maftoaxt 2024-07-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt 469 ucsc-maftoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing 2018-03-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 Genetic variation analysis Genetics, Genetic variation, Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 11761 12093 873 889 5762 5762 473 473 5610 5610 343 343 23133 23465 1689 1705 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 False -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 False -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run 2021-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 9 9 0 0 0 0 0 0 0 0 24 24 9 9 False -manta manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta 2023-06-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 218 218 34 34 0 0 0 0 0 0 0 0 218 218 34 34 False -map_param_value map_param_value Map a parameter value to another value To update Text Manipulation map_param_value 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3780 3780 67 67 1012 1012 57 57 105 105 3 3 4897 4897 127 127 False -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 False -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer 2023-12-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 0 0 0 0 0 0 0 0 8 8 2 2 False -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 False -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 False -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 743 816 103 141 292 2868 82 459 0 0 0 0 1035 3684 185 600 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 False -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme 2018-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.5.6 meme 5.5.7 Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability 3 0 4 0 3 0 4 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 20990 22979 762 892 10975 25929 1551 3249 0 0 0 0 31965 48908 2313 4141 False -meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip 2018-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6413 7000 705 743 7260 7260 1171 1171 0 0 0 0 13673 14260 1876 1914 False -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco 2018-06-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 565922 566630 418 441 45844 107523 671 4353 19828 19994 100 137 631594 694147 1189 4931 False -merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 20905 31051 1906 2128 21780 132833 885 3172 1524 1925 122 152 44209 165809 2913 5452 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin 2020-04-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 Haplotype mapping GWAS study, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 False -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 False -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 False -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 False -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 False -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 False -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 False -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 False -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit 2016-12-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -mgf_formatter mgf_formatter Up-to-date mgf_formatter 2014-09-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 False -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 False -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 False -mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 8 8 17 63 6 19 0 0 0 0 26 74 14 27 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 2018-08-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 Pairwise sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 346530 349075 4323 4419 108535 108535 4075 4075 22331 22331 1166 1166 477396 479941 9564 9660 False -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 False -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 False -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 False -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko 2018-04-12 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 False -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 False -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 False -moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs 2019-07-28 iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 339 339 56 56 0 0 0 0 0 0 0 0 339 339 56 56 False -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 False -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mosdepth mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth 2022-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1278 1278 87 87 168 168 24 24 102 102 5 5 1548 1548 116 116 False -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 False -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 False -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 False -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 False -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 False -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 False -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps 2017-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 485 871 159 298 0 0 0 0 485 871 159 298 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 False -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 False -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 False -mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 49 5 5 81 417 23 118 0 0 0 0 125 466 28 123 False -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns 2020-10-19 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 False -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 False -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish 2018-06-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 9284 9694 215 229 0 0 0 0 2358 2358 49 49 11642 12052 264 278 False -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 False -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 False -ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download 2019-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6873 6873 1664 1664 17651 17651 4513 4513 6228 6228 972 972 30752 30752 7149 7149 False -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 False -ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.20.0 ncbi-datasets-cli Data handling, Sequence database search, Data retrieval Biological databases 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4417 4417 1024 1024 6940 6940 2275 2275 1 1 1 1 11358 11358 3300 3300 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct 2022-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 22.4 entrez-direct 22.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 3 0 2 False -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils 2020-08-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 4 0 0 4 0 0 0 2 0 0 0 0 0 0 0 7 7 0 2794 3191 533 664 0 0 0 0 0 0 0 0 2794 3191 533 664 False -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 False -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr 2022-08-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 6 6 0 0 0 0 0 0 0 0 12 12 6 6 False -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 False -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr 2020-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1403 1403 49 49 0 0 0 0 0 0 0 0 1403 1403 49 49 False -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM 2015-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24611 29662 633 716 15523 21395 740 1128 7751 8972 125 145 47885 60029 1498 1989 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 False -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ococo ococo Variant detection of SNVs To update https://github.com/karel-brinda/ococo Variant Analysis ococo 2017-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1850 1963 79 93 1370 1370 194 194 0 0 0 0 3220 3333 273 287 False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit 2017-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 582 663 68 69 0 0 0 0 0 0 0 0 582 663 68 69 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 False -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 False -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe 2022-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 False -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader Data Source packaged_annotation_loader 2022-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 False -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp 2022-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 Variant calling Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 2022-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.14.99 pbmm2 1.14.99 Pairwise sequence alignment, Sorting Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 17 17 0 0 0 0 0 0 0 0 70 70 17 17 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram 2016-06-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.2 openjdk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5505 5505 510 510 7932 8582 811 909 736 736 119 119 14173 14823 1440 1538 False -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 False -peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla 2024-02-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 False -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 False -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 False -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 False -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 False -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 False -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools 2017-09-28 bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat 2022-01-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 109 109 29 29 250 250 84 84 0 0 0 0 359 359 113 113 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 False -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard 2019-05-30 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.3.0 Formatting Sequencing 31 31 31 31 31 31 31 31 0 0 0 0 0 0 0 0 31 4 31 0 0 31 0 0 0 31 0 0 0 0 0 0 31 31 31 0 386934 399039 11024 11956 366646 589980 32000 57111 56622 62258 2845 3398 810202 1051277 45869 72465 False -pick_value pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value 2023-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1607 1607 41 41 490 490 53 53 127 127 4 4 2224 2224 98 98 False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 False -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 False -pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval 2015-03-06 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 613 640 48 54 1381 7804 201 1552 756 815 22 30 2750 9259 271 1636 False -pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3639 3774 414 461 9754 52522 1247 4531 1893 2433 191 318 15286 58729 1852 5310 False -pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update https://github.com/broadinstitute/pilon/wiki Variant Analysis pilon 2016-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 Sequence assembly, Analysis Assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9045 9458 1115 1144 7989 7989 1070 1070 3945 4137 726 741 20979 21584 2911 2955 False -pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel 2021-09-29 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign 2019-08-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1245 1245 231 231 9046 9046 630 630 0 0 0 0 10291 10291 861 861 False -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 False -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 False -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 False -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink 2020-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 Genetic variation analysis GWAS study 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 851 851 127 127 249 249 43 43 0 0 0 0 1100 1100 170 170 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 False -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 False -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat 2020-03-24 nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment 2016-11-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment 2016-11-07 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 False -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 False -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 False -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 False -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 False -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 False -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 False -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 False -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 False -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 False -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 False -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 False -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 False -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 False -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 False -protxml_to_xls protxml_to_xls To update protxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_eval psm_eval To update psm_eval 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 False -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2716 2716 104 104 134 134 43 43 40 40 1 1 2890 2890 148 148 False -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 False -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -pyvo_integration astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy To update Data Source astronomicalarchivestool 2023-08-26 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0.10.0 astropy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 6 6 0 0 0 0 0 0 0 0 53 53 6 6 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 False -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 False -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 False -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 False -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 False -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 False -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -query query Execute an SQL statement on a set of tables To update Text Manipulation query 2020-12-09 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -query_impc query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc 2023-10-11 iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular Text Manipulation 2017-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.1 python 3 3 3 1 3 3 3 1 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 130124 135361 1265 1305 11135 11135 922 922 5939 5939 153 153 147198 152435 2340 2380 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 False -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 False -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 False -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 False -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 False -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 False -regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace 2017-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 78648 78834 1144 1156 18063 18063 870 870 4455 6051 194 289 101166 102948 2208 2315 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 148572 169964 3525 3682 36694 113826 3910 8163 9713 10577 1475 1598 194979 294367 8910 13443 False -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 False -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file 2017-02-24 bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 577184 577312 463 492 43900 44233 283 373 2190 2190 112 112 623274 623735 858 977 False -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names 2017-05-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 514 573 69 83 0 0 0 0 0 0 0 0 514 573 69 83 False -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 415 721 128 219 0 0 0 0 415 721 128 219 False -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3543 3619 108 111 536 536 157 157 0 0 0 0 4079 4155 265 268 False -resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window 2016-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 86 8 9 138 216 30 57 0 0 0 0 213 302 38 66 False -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam 2019-04-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.21 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 11 11 520 520 31 31 0 0 0 0 560 560 42 42 False -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 False -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 False -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 False -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 False -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 False -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 False -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 False -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 False -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor 2023-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths 2022-10-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign 2022-03-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba 2022-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools 2022-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser 2022-06-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps 2016-01-29 earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 False -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1155 1251 57 63 2264 18187 189 1748 525 590 10 17 3944 20028 256 1828 False -sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python 1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 278 12 26 3554 76029 450 6346 229 345 16 29 3879 76652 478 6401 False -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba 2020-05-19 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 684 684 17 17 684 684 17 17 False -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! Up-to-date https://github.com/biod/sambamba SAM sambamba 2016-06-23 bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 1.0.1 sambamba 1.0.1 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 297 297 51 51 0 0 0 0 0 0 0 0 297 297 51 51 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools To update https://github.com/samtools/samtools SAM 2021-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.20 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa 2020-12-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.2 sansa 0.2.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 138 138 36 36 0 0 0 0 0 0 0 0 138 138 36 36 False -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 False -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 False -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol 2022-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scaffold scaffold, scaffold_export To update scaffold 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 False -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -scripting singularity_scriptrunner suite_scripting To update https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ Text Manipulation scripting tools 2023-07-29 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr 2020-02-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5106 5106 116 116 6419 6419 241 241 0 0 0 0 11525 11525 357 357 False -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 281 2284 10 53 0 0 0 0 0 0 0 0 281 2284 10 53 False -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign 2024-04-18 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.7 segalign-galaxy 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 252 252 47 47 0 0 0 0 252 252 47 47 False -segemehl segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1095 1306 98 113 0 0 0 0 0 0 0 0 1095 1306 98 113 False -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 False -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 False -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 False -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 False -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 False -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sgwb sgwb_astro_tool SGWB To update Astronomy sgwb_astro_tool 2024-04-17 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0.0.1+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 0 0 0 0 0 0 0 0 5 5 2 2 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 64 4 4 0 0 0 0 0 0 0 0 54 64 4 4 False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 27232 36366 2184 2789 16648 84460 4191 18767 2785 3276 373 452 46665 124102 6748 22008 False -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1620 2660 378 589 10551 24579 682 1851 284 398 67 83 12455 27637 1127 2523 False -sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 276 379 30 42 972 9053 146 1008 644 689 5 7 1892 10121 181 1057 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext 2021-02-28 iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 0 2 4 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 220 220 68 68 0 0 0 0 416 416 10 10 636 636 78 78 False -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 False -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 False -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes 2019-04-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 False -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 False -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 False -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists 2019-10-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6555 6555 807 807 5336 5336 171 171 1143 1143 182 182 13034 13034 1160 1160 False -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites 2017-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6597 6597 663 663 1467 1467 256 256 1279 1279 114 114 9343 9343 1033 1033 False -snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff 2018-07-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 5 5 5 5 5 5 5 5 0 0 0 0 0 1 0 0 0 5 5 0 0 5 0 0 0 5 0 0 0 0 0 0 5 5 5 0 103826 108296 7181 7908 115727 178110 15871 22769 11817 13155 2148 2321 231370 299561 25200 32998 False -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 SNP detection DNA polymorphism, Nucleic acid sites, features and motifs 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 764895 764895 1276 1276 94572 94572 1636 1636 26990 26990 561 561 886457 886457 3473 3473 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region To update https://github.com/BrownfieldPlantLab/SNPFreqPlot Variant Analysis snpfreqplot 2020-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 3683 3683 338 338 1401 1401 433 433 1029 1029 95 95 6113 6113 866 866 False -snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift 2015-04-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 8 8 8 8 8 8 8 8 0 0 0 0 0 8 0 0 0 0 8 0 0 8 0 0 0 8 0 0 0 0 0 0 8 8 8 0 5142904 5146618 3602 4283 382391 421190 7013 9678 104030 105024 960 1184 5629325 5672832 11575 15145 False -snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 52 55 23 24 421 421 75 75 0 0 0 0 473 476 98 99 False -snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 509 554 107 128 474 474 190 190 0 0 0 0 983 1028 297 318 False -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv 2021-03-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 False -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_file_on_column tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5995 6261 408 453 2150 2150 311 311 26 26 2 2 8171 8437 721 766 False -split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection 2019-08-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16415 16623 968 984 9133 9133 672 672 4140 4140 148 148 29688 29896 1788 1804 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta 2015-10-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1772 1811 278 294 3012 3012 564 564 0 0 0 0 4784 4823 842 858 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 False -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 False -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 False -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 False -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign 2022-10-02 iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka 2021-01-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 669 669 112 112 1261 1261 417 417 0 0 0 0 1930 1930 529 529 False -stress_ng stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng 2021-03-04 bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 3 3 0 0 0 0 0 0 0 0 62 62 3 3 False -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 False -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 False -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 False -subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 566512 567199 410 470 49985 184650 1473 7631 20648 20897 155 188 637145 772746 2038 8289 False -subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1178 1450 124 141 3169 40539 636 3435 799 950 26 38 5146 42939 786 3614 False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 False -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 False -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib 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qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 False -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 False -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 False -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 False -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 False -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 False -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 False -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 False -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 False -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink 2017-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 False -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 False -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar 2013-12-02 devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16526 64515 2803 7456 0 0 0 0 16526 64515 2803 7456 False -table_compute table_compute Perform general-purpose table operations To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute Text Manipulation table_compute 2019-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 216072 216115 1811 1814 12326 12326 1558 1558 16136 16136 256 256 244534 244577 3625 3628 False -tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2188 2220 33 38 0 0 0 0 0 0 0 0 2188 2220 33 38 False -tabular_to_fasta tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 329032 333057 1489 1702 79033 215770 2441 8587 27876 33727 296 360 435941 582554 4226 10649 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 False -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 False -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 False -tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter 2019-10-03 iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22977 22977 461 461 3888 3888 274 274 3611 3611 80 80 30476 30476 815 815 False -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 False -tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.1 tbvcfreport 1.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2955 2955 335 335 6090 6090 348 348 2347 2347 72 72 11392 11392 755 755 False -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 False -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 False -text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing 2019-01-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 20 20 20 20 20 20 20 20 0 0 0 0 0 0 0 0 19 1 19 0 0 19 0 0 0 20 0 0 0 0 0 0 19 19 19 0 3898014 4015573 37698 42095 648268 915282 47636 69828 103365 105214 7778 7953 4649647 5036069 93112 119876 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 False -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 False -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 False -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 False -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 False -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 False -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update 2021-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.8 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 3314 3314 124 124 0 0 0 0 0 0 0 0 3314 3314 124 124 False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 False -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 False -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 False -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler 2019-04-15 nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmer trimmer Trim leading or trailing characters. To update Text Manipulation trimmer 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 5304 7438 447 512 15698 108672 658 2946 266 822 53 81 21268 116932 1158 3539 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 False -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services 2018-06-20 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 255 379 31 37 281 281 64 64 0 0 0 0 536 660 95 101 False -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa 2016-08-19 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 469 ucsc-twobittofa 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 413 511 84 118 441 441 123 123 21 21 2 2 875 973 209 243 False -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 False -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 False -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_axttomaf 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf 469 ucsc-axttomaf 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 False -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_nettoaxt 2024-09-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt 469 ucsc-nettoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 False -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 False -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 False -unzip unzip Unzip file To update https://github.com/bmcv Convert Formats unzip 2019-08-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 6.0 unzip 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6942 7024 1345 1356 1 1 1 1 2461 2461 266 266 9404 9486 1612 1623 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 False -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 False -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java 2020-08-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 381 381 37 37 0 0 0 0 0 0 0 0 381 381 37 37 False -variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer 2019-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 95 95 14 14 516 516 67 67 0 0 0 0 611 611 81 81 False -varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan 2018-11-29 iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 10711 11502 1442 1560 16705 16705 3135 3135 1036 1036 100 100 28452 29243 4677 4795 False -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf 2022-11-28 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 2013-11-17 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5058 6139 606 699 17232 53268 2965 5686 2298 2656 424 482 24588 62063 3995 6867 False -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 False -vcf2maf vcf2maf vcf2maf: Convert VCF into MAF To update https://github.com/mskcc/vcf2maf Convert Formats vcf2maf 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1097 1097 46 46 0 0 0 0 65 65 5 5 1162 1162 51 51 False -vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 221 57 65 1399 2700 209 584 0 0 0 0 1590 2921 266 649 False -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 169090 169679 823 874 16304 42215 1141 2594 2485 2511 169 172 187879 214405 2133 3640 False -vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 263 340 31 54 263 342 31 56 False -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 513 569 6 9 513 569 6 9 False -vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 400 455 129 140 0 0 0 0 238 606 19 56 638 1061 148 196 False -vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 3 0 0 0 0 335 463 19 28 335 482 19 31 False -vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 882 888 30 32 6118 8261 36 114 175 184 6 6 7175 9333 72 152 False -vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6879 17157 897 1219 7585 14509 1245 1925 1648 1681 225 229 16112 33347 2367 3373 False -vcfanno vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 SNP annotation Genetic variation, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1139 1139 174 174 0 0 0 0 0 0 0 0 1139 1139 174 174 False -vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2797 2850 157 181 3668 14532 652 1392 494 507 61 63 6959 17889 870 1636 False -vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 203 62 66 497 1828 155 387 184 197 11 11 870 2228 228 464 False -vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3017 4049 185 210 4709 20250 406 1147 507 527 40 42 8233 24826 631 1399 False -vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 416 478 35 40 3969 10457 82 309 362 378 8 8 4747 11313 125 357 False -vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 767 96 106 803 1895 222 627 241 256 16 17 1789 2918 334 750 False -vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1422 2020 284 505 4951 19530 1021 2669 493 516 60 62 6866 22066 1365 3236 False -vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 233 253 37 42 234 1839 79 287 199 214 11 12 666 2306 127 341 False -vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 572 585 90 92 2063 2427 139 296 272 290 19 22 2907 3302 248 410 False -vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37489 47142 2113 2218 75128 162296 5730 10533 2626 2736 320 331 115243 212174 8163 13082 False -vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 926 957 155 173 2291 5323 313 985 251 265 28 31 3468 6545 496 1189 False -vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 172 183 21 25 351 879 67 201 312 342 15 16 835 1404 103 242 False -vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 778 794 107 112 2414 3721 179 508 209 225 20 21 3401 4740 306 641 False -vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 502 555 134 143 3428 6338 266 858 220 235 23 24 4150 7128 423 1025 False -vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1964 1991 182 186 1937 3846 188 644 567 601 26 27 4468 6438 396 857 False -vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 269 310 38 42 358 1071 89 287 179 213 12 14 806 1594 139 343 False -vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 711 28 33 403 831 75 200 190 214 10 12 1183 1756 113 245 False -vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 168 13 15 153 350 27 75 184 192 6 6 498 710 46 96 False -vcfselectsamples vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 830 900 69 88 1315 6257 237 959 344 363 20 21 2489 7520 326 1068 False -vcfsort vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1868 1904 174 185 18378 24175 422 1279 537 674 70 73 20783 26753 666 1537 False -vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 192 81 90 1853 3943 581 1280 144 156 13 16 2152 4291 675 1386 False -vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 440 594 127 142 0 0 0 0 0 16 0 12 440 610 127 154 False -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus 2016-10-16 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcftools_isec vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 537 104 118 0 1 0 1 39 496 28 48 418 1034 132 167 False -vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 817 1084 244 273 0 0 0 0 93 448 44 60 910 1532 288 333 False -vcftools_slice vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 423 56 60 6261 8115 133 362 127 157 10 19 6798 8695 199 441 False -vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 142 46 49 0 0 0 0 120 142 12 19 254 284 58 68 False -vcfvcfintersect vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 976544 977015 703 748 64155 81830 981 2103 11044 11069 225 229 1051743 1069914 1909 3080 False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 False -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 False -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 False -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -weblogo3 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 2017-11-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2720 2818 206 228 10299 30578 1354 3657 1226 1285 50 59 14245 34681 1610 3944 False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 False -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig 2024-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 469 ucsc-wigtobigwig 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1601 1601 106 106 1108 1108 172 172 200 200 15 15 2909 2909 293 293 False -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 False -winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap 2021-04-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 279 279 46 46 12 12 4 4 0 0 0 0 291 291 50 50 False -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 False -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 False -xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet 2021-10-18 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 17 17 0 0 0 0 0 0 0 0 59 59 17 17 False -xpath xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 235 7 8 0 1 0 1 0 0 0 0 128 236 7 9 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 False -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 False -zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 96 9 12 0 0 0 0 0 0 0 0 83 96 9 12 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False +Galaxy wrapper id Description To keep Deprecated +10x_bamtofastq Converts 10x Genomics BAM to FASTQ +2d_auto_threshold Automatic thresholding +2d_feature_extraction 2D feature extraction +2d_filter_segmentation_by_features filter segmentation by rules +2d_histogram_equalization 2d histogram equalization +2d_simple_filter 2d simple filter +AggregateAlignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. +AlignCluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. +CMFinder Determines consensus motives for sequences. +CollectResults Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. +CollectResultsNoAlign Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. +EMLassemblyline Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa +Ecoregionalization_workflow Tools to compute ecoregionalization with BRT model predictions and clustering. +Ensembl-REST A suite of Galaxy tools designed to work with Ensembl REST API. +GAFA Gene Align and Family Aggregator +GSPAN Second step of GraphClust +Geom_mean_workflow Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). +LocARNAGraphClust MLocARNA computes a multiple sequence-structure alignment of RNA sequences. +NSPDK Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. +PAMPA Tools to compute and analyse biodiversity metrics +Plotting Plotting results for GraphClust +PrepareForMlocarna This tool prepares files for locarna step. +Preprocessing Preprocessing input for GraphClust +Structure_GSPAN Convert RNA structure to GSPAN graphs +ThermoRawFileParser Thermo RAW file converter +TreeBest TreeBeST best +TrimNs TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline +ab1_fastq Tool to convert ab1 files into FASTQ files +abacas Order and Orientate Contigs +abricate Mass screening of contigs for antiobiotic resistance genes +abritamr A pipeline for running AMRfinderPlus and collating results into functional classes +abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler +adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. +add_input_name_as_column Add input name as column on an existing tabular file +add_line_to_file Adds a text line to the beginning or end of a file. +add_value Add a value as a new column. +aegean AEGeAn toolkit wrappers +agat GTF/GFF analysis toolkit +aldex2 Performs analysis Of differential abundance taking sample variation into account +align_back_trans Thread nucleotides onto a protein alignment (back-translation) +allegro Linkage and haplotype analysis from deCODE +ambertools Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. +amplican AmpliCan is an analysis tool for genome editing. +ampvis2 ampvis2 +amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." +ancombc Performs analysis of compositions of microbiomes with bias correction. +anisotropic_diffusion Anisotropic image diffusion +anndata Import, Export, Inspect and Manipulate Anndata and Loom objects +annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages +antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . +antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters +apoc Large-scale structural comparison of protein pockets +apollo Access an Apollo instance from Galaxy +appendfdr +aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. +aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. +aresite2 AREsite2 REST Interface +argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database +arriba Arriba detects fusion genes in RNA-Seq data after running RNA-STAR +art Simulator for Illumina, 454, and SOLiD sequencing data +artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis +artic The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building +askomics Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ +askor AskoR links EdgeR and AskOmics +assembly-stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. +assemblystats Summarise an assembly (e.g. N50 metrics) +astral Tool for estimating an unrooted species tree given a set of unrooted gene trees +astropytools AstropyTools library contains Galaxy tools for elementary Astrophysical operations +atactk_trim_adapters Trim adapters from paired-end HTS reads. +augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. +augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. +b2btools This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. +background_removal Background removal filters using scikit-image +bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" +bam2mappingstats Generates mapping stats from a bam file. +bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. +bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. +bamhash Hash BAM and FASTQ files to verify data integrity +bamparse Generates hit count lists from bam alignments. +bamtools Operate on and transform BAM datasets in various ways using bamtools +bamtools_filter Filter BAM datasets on various attributes using bamtools filter +bamtools_split Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. +bamutil bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. +bandage Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily +barcode_collapse Paired End randomer aware duplicate removal algorithm +barcode_splitter A utility to split sequence files using multiple sets of barcodes +baredsc baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. +baric_archive A data source tool to fetch data from a BARIC Archive server. +barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. +basecoverage Base Coverage of all intervals +baseline_calculator Toxicity prediction using QSAR models +basil Breakpoint detection, including large insertions +batched_lastz Galaxy wrapper for the batching Lastz runs +bax2bam BAX to BAM converter +bayescan Detecting natural selection from population-based genetic data +bbgbigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. +bbtools BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. +bcftools BCFtools toolkit wrappers +bctools bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 +beacon2 beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). +beacon2-import Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. +beagle Beagle is a program for phasing and imputing missing genotypes. +bed_to_protein_map Converts a BED file to a tabular list of exon locations +bedops BEDOPS: high-performance genomic feature operations +bedtools bedtools is a powerful toolset for genome arithmetic +bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. +berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. +best_regression_subsets Perform Best-subsets Regression +bfconvert Convert image +bia-ftplinks Tool to query ftp links for study from bioimage archive +bigscape Construct sequence similarity networks of BGCs and groups them into GCF +bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files +bigwig_to_bedgraph Convert from bigWig to bedGraph format +bigwig_to_bedgraph Converts a bigWig file to bedGraph format +bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format +binary2labelimage Binary 2 label image +binaryimage2points Binary Image to Points +binning_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. +bio3d Bio3d is a program that can be used to analyse molecular dynamics trajectories. +bioext A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! +bioformats2raw Convert image to OME-Zarr +biohansel Heidelberg and Enteritidis SNP Elucidation +biohansel_bionumeric_converter Convert BioHansel output data to a Bionumerics friendly form +bioimaging Load model from BioImage.IO and make inferences +bioinformatics_cafe Miscellanea of scripts for bioinformatics +biom_format The biom-format package provides a command line interface and Python API for working with BIOM files. +biomodelsML Wrappers for tools to bring BioModels AI models into Galaxy. +biomoldyn Tools for MD analysis +bionano Bionano Solve is a set of tools for analyzing Bionano data +bioperl Converts GenBank format files to GFF3 +biotradis Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. +biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. +biscot Bionano scaffolding correction tool +bismark A tool to map bisulfite converted sequence reads and determine cytosine methylation states +blast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome +blast2go Maps BLAST results to GO annotation terms +blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input +blast_plus_remote_blastp NCBI BLAST+ with -remote option +blast_rbh BLAST Reciprocal Best Hits (RBH) from two FASTA files +blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs +blast_unmatched Extract unmatched query sequences from blast +blastparser_and_hits Parse blast outputs and compile hits +blastx_to_scaffold Generate DNA scaffold from blastx alignment of Contigs +blastxml_to_gapped_gff3 BlastXML to gapped GFF3 +blastxml_to_top_descr Make table of top BLAST match descriptions +blat_coverage_report Polymorphism of the Reads +blat_mapping Coverage of the Reads in wiggle format +blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. +blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. +blockclust BlockClust detects transcripts with similar processing patterns. +bowtie2 Bowtie2: Fast and sensitive read alignment +bowtie_wrappers Galaxy wrappers for the Bowtie short read mapping tools. +bracken Bayesian Reestimation of Abundance with KrakEN +braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . +braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . +breseq Predicts mutations in microbial genomes +brew3r_r Extend 3' end of a GTF using another GTF as a template +bumbershoot +bundle_collections Tool to bundle up list collection into a single zip to be download +busco BUSCO assess genome and annotation completeness +bwa Wrapper for bwa mem, aln, sampe, and samse +bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. +bwameth Fast and accurate alignment of BS-seq reads +c3s Copernicus Climate Change Service (C3S) +cactus Cactus is a reference-free whole-genome multiple alignment program +cads Copernicus Atmosphere Data Store (ADS) +calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. +calculate_numeric_param Calculate a numeric parameter value using integer and float values. +calisp Calgary approach to isotopes in proteomics +camera +cami_amber Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments +canonical_correlation_analysis Canonical Correlation Analysis +canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). +cap3 cap3 wrapper +cardinal Statistical and computational tools for analyzing mass spectrometry imaging datasets +cat Contig Annotation Tool (CAT) +categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. +ccat Control-based ChIP-seq Analysis Tool +cd_hit_dup simple tool for removing duplicates from sequencing reads +cdhit Cluster or compare biological sequence datasets +cdo CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. +cell-types-analysis Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis +cellpose Cellpose is an anatomical segmentation algorithm +cellprofiler cellProfiler wrapper +cellprofiler_v4 cellProfiler4 wrapper +cemitool Gene co-expression network analysis tool +cesm Community Earth System Model (CESM) +cfm Competitive Fragmentation Modeling (CFM) +chado Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado +champ_blocs Compute indicators for turnover boulders fields +change_case Convert column case. +charts Enables advanced visualization options in Galaxy Charts +chatgpt Using the OpenAI GPT models to generate text based on user input. +checkm Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes +checkv Assess quality of single-contig viral genomes +cherri Computational Help Evaluating RNA-RNA interactions +cherry_pick_fasta Pick fasta sequence with specific header content +chewbbaca BSR-Based Allele Calling Algorithm +chipseeker A tool for ChIP peak annotation and visualization +chira Chimeric Read Annotator for RNA-RNA interactome data +chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing +chromeister ultra-fast pairwise genome comparisons +chromosome_diagram Chromosome Diagrams using Biopython +circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) +circexplorer2 Comprehensive and integrative circular RNA analysis toolset. +circos Build Circos Plots in Galaxy +cite_seq_count Count CMO/HTO +clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling +clc_assembly_cell Galaxy wrapper for the CLC Assembly Cell suite from CLCBio +climate-stripes Create climate stripes from a tabular input file +clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins +clustalw ClustalW multiple sequence alignment program for DNA or proteins +cluster Cluster the intervals of a dataset +clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy +cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. +cmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. +cnv-phenopacket cnv-phenopacket Converts TSV metadata file to JSON. +cnv-vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. +cnvkit detecting copy number variants and alterations genome-wide from high-throughput sequencing +codeml Detects positive selection +cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. +cojac co-occurrence of mutations on amplicons +colabfold Protein prediction based on AlphaFold2 +colibread Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome +collapse_collection Collection tool that collapses a list of files into a single datasset in order of appears in collection +collection_column_join Column Join on Collections +collection_element_identifiers Extract element identifiers of a collection +color_deconvolution Color-deconvolution methods +colorize_labels Colorize label map +column_arrange_by_header Column arrange by header name +column_maker Compute an expression on every row +column_order_header_sort Sort Column Order by heading +column_remove_by_header Remove columns by header +combineJSON JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. +combine_assembly_stats Combine multiple Assemblystats datasets into a single tabular report +combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances +combine_tabular_collection Combine Tabular Collection into a single file +compalignp Compute fractional identity between trusted alignment and test alignment +compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information +compleasm Compleasm: a faster and more accurate reimplementation of BUSCO +complement Complement intervals of a dataset +compose_text_param Compose a text parameter value using text, integer and float values +compress_file Compress files. +compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. +compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. +compute_q_values Compute q-values based on multiple simultaneous tests p-values +concat Concatenate two bed files +concat_channels Concatenate images +concat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. +concat_paired Concatenate paired datasets +concoct CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. +condense_characters Condense consecutive characters. +consensus_from_alignments Tool to compute a consensus sequence from several aligned fasta sequences +consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment +convert_characters Convert delimiters to tab. +convert_solid_color2nuc Convert Color Space to Nucleotides +cooler cooler different tools to process Hi-C from mirnylab +coordinates_of_roi Coordinates of ROI +coprarna Target prediction for prokaryotic trans-acting small RNAs +correlation Correlation for numeric columns +correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis +cosg Marker gene identification for single-cell sequencing data using COSG. +count_gff_features Count GFF Features +count_objects Count Objects +count_roi_variants Count sequence variants in region of interest in BAM file +coverage Coverage of a set of intervals on second set of intervals +coverage_report Generate Detailed Coverage Report from BAM file +coverage_stats BAM coverage statistics using samtools idxstats and depth +coverm CoverM genome and contig wrappers +cpat Coding-potential assessment tool using an alignment-free logistic regression model. +cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts +crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. +crosscontamination_barcode_filter Barcode contamination discovery tool +crossmap CrossMap converts genome coordinates or annotation files between genome assemblies +crt CRISPR Recognition Tool +cryptogenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. +csvtk Rapid data investigation and manipulation of csv/tsv files +cta Basic simulation of CTA telescope observations using gammapy package +ctd_batch CTD analysis of chemicals, diseases, or genes +cuffcompare Galaxy wrappers for the Cuffcompare tool. +cuffdiff Galaxy wrappers for the Cuffdiff tool. +cufflinks Galaxy wrappers for the Cufflinks tool. +cuffmerge Galaxy wrappers for the Cuffmerge tool. +cuffnorm The Cuffnorm tool +cuffquant The Cuffquant tool +cummerbund Wrapper for the Bioconductor cummeRbund library +cummerbund_to_tabular Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. +curve_fitting Polynomial curve fitting to data points +custom_pro_db CustomProDB +custom_pro_db_annotation_data_manager CustomProDB Annotation +cut_columns Select columns from a dataset. +cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). +cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. +cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. +dada2 DADA2 wrappers +das_tool DAS Tool for genome resolved metagenomics +data-hca Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects +data-scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home +data_exploration Explore data through multiple statistical tools +data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper +data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper +data_source_iris_tcga IRIS-TCGA Data source tool +datamash GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. +dbbuilder Protein Database Downloader +decontam Removes decontamination features (ASVs/OTUs) using control samples +decontaminator Deep Learning method for novel virus detection in sequencing data +decoupler decoupler - Ensemble of methods to infer biological activities +decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. +deepmicro Representation learning and classification framework +deepsig Predictor of signal peptides in proteins based on deep learning +deepvariant DeepVariant is a deep learning-based variant caller +deg_annotate Annotate DESeq2/DEXSeq output tables +delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file +delly Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. +deseq2 Differential gene expression analysis based on the negative binomial distribution +deseq2_normalization Normalizes gene hitlists +detection_viz Detection Visualization +dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data +dexseq Inference of differential exon usage in RNA-Seq +dgidb_annotator Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) +dia_umpire DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics +dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. +diamond DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. +diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. +diapysef diapysef is a convenience package for working with DIA-PASEF data +diff GNU diff tool that calculates the differences between two files. +diffacto Diffacto comparative protein abundance estimation +diffbind Diffbind provides functions for processing ChIP-Seq data. +diffbind Diffbind provides functions for processing ChIP-Seq data. +digestdb +dimet DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. +directag_and_tagrecon +disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler +divide_pg_snp Separate pgSnp alleles into columns +dnabot DNA assembly using BASIC on OpenTrons +dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. +dorina data source for RNA interactions in post-transcriptional regulation +dose_responses A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses +dot2ct Dot-Bracket to Connect Table (CT) +dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence +dram DRAM for distilling microbial metabolism to automate the curation of microbiome function +draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria +drep dRep compares and dereplicates genome sets +droplet-barcode-plot Make a cell barcode plot for droplet single-cell RNA-seq QC +dropletutils De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 +dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data +dwt_cor_ava_perclass Compute P-values and Correlation Coefficients for Feature Occurrences +dwt_cor_avb_all Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features +dwt_ivc_all Compute P-values and Second Moments for Feature Occurrences +dwt_var_perclass Compute P-values and Max Variances for Feature Occurrences +dwt_var_perfeature Wavelet variance using Discrete Wavelet Transfoms +ear A tool to compile assembly reports and stastics from assembly pipeline +ebi_tools Tools to query and download data from several EMBL-EBI databases +ectyper EC-Typer - in silico serotyping of Escherichia coli species +edger Perform RNA-Seq differential expression analysis using edgeR pipeline +edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. +effectiveT3 Find bacterial type III effectors in protein sequences +eggnog_mapper eggnog-mapper fast functional annotation of novel sequences +egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing +embl2fa Converts EMBL flat format to fasta format +emboss_5 Galaxy wrappers for EMBOSS version 5.0.0 tools +ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). +enasearch A Python library for interacting with ENA's API +encyclopedia Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis +ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions +eodie Earth Observation Data Information Extractor +epicseg EpiCSeg is a tool for conducting chromatin segmentation. +episcanpy EpiScanpy – Epigenomics single cell analysis in python +essential_climate_variables Get Copernicus Essential Climate Variables for assessing climate variability +ete Analyse phylogenetic trees using the ETE Toolkit +evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. +exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data +exonerate Exonerate is a generic tool for pairwise sequence comparison. +exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. +export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn +export_to_cluster Export datasets to cluster +express Quantify the abundances of a set of target sequences from sampled subsequences +extract_genomic_dna Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. +ez_histograms ggplot2 histograms and density plots +falco A high throughput sequence QC analysis tool +fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) +fasplit faSplit is a tool to split a single FASTA file into several files +fasta2bed Convert multiple fasta file into tabular bed file format +fasta_clipping_histogram Length Distribution chart +fasta_compute_length Compute sequence length +fasta_concatenate_by_species Concatenate FASTA alignment by species +fasta_extract extract single fasta from multiple fasta file +fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) +fasta_filter_by_length Filter sequences by length +fasta_formatter FASTA Width formatter +fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together +fasta_nucleotide_changer RNA/DNA converter. +fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. +fasta_stats Display summary statistics for a fasta file. +fasta_to_tabular FASTA-to-Tabular converter +fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity +fastg2protlib Generate FASTA from FASTG +fastk FastK: A K-mer counter (for HQ assembly data sets) +fastp Fast all-in-one preprocessing for FASTQ files +fastq_combiner Combine FASTA and QUAL into FASTQ +fastq_filter Filter FASTQ reads by quality score and length +fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) +fastq_groomer Convert between various FASTQ quality formats. +fastq_info FASTQ info allows to validate single or paired fastq files +fastq_manipulation Manipulate FASTQ reads on various attributes. +fastq_masker_by_quality FASTQ Masker by quality score +fastq_pair Paired-end fastq pairer +fastq_pair_names Extract FASTQ paired read names +fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. +fastq_paired_end_interlacer FASTQ interlacer on paired end reads +fastq_paired_end_joiner FASTQ joiner on paired end reads +fastq_paired_end_splitter FASTQ splitter on joined paired end reads +fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads +fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. +fastq_quality_boxplot Draw quality score boxplot +fastq_quality_converter Quality format converter (ASCII-Numeric) +fastq_quality_filter Filter by quality +fastq_quality_trimmer FASTQ trimmer based on quality +fastq_stats FASTQ Summary Statistics by column +fastq_to_fasta FASTQ to FASTA converter +fastq_to_tabular FASTQ to Tabular converter +fastq_trimmer FASTQ Trimmer by quality +fastq_trimmer_by_quality FASTQ Quality Trimmer by sliding window +fastq_utils Set of tools for handling fastq files +fastqc Read QC reports using FastQC +fastqc_stats Summary multiple FastQC into a single tabular line report +fastqe FASTQE +fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data +fastqtofasta FASTQ to FASTA converter +fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL +fastx_artifacts_filter Remove sequencing artifacts +fastx_barcode_splitter Barcode Splitter +fastx_clipper Clip adapter sequences +fastx_collapser Collapse sequences +fastx_nucleotides_distribution Draw nucleotides distribution chart +fastx_quality_statistics Compute quality statistics +fastx_renamer Rename sequences +fastx_reverse_complement Reverse-Complement +fastx_trimmer Trim sequences +fates-emerald EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model +fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs +feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy +featurecounter Feature coverage +featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome +feelnc Galaxy wrapper for FEELnc +feelnc2asko Convert FeelNC GTF to GFF3 +feht Automatically identify makers predictive of groups. +fermikit FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. +fetch_fasta_from_ncbi Fetch fasta sequences from NCBI using eutils wrappers +fgsea Perform gene set testing using fgsea +file_manipulation This tool returns all unique lines from a tab-separated file. +filter_by_fasta_ids Filter FASTA on the headers and/or the sequences +filter_compounds Tool for filtering organometallics/anorganic compounds from a list of compounds. +filter_density Filter out position based on distance between SNVs +filter_spades_repeats Remove short and repeat contigs/scaffolds +filter_stats SNVPhyl filter_stats +filter_transcripts_via_tracking Filter Combined Transcripts +filter_vcf SNVPhyl filter_vcf +filtlong Filtlong - Filtering long reads by quality +find_diag_hits Find diagnostic hits +find_repeats Find repetitive regions on a reference genome using MUMMer +find_subsequences +fisher_test Fisher's exact test on two-column hit lists. +flair FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. +flanking_features Fetch closest non-overlapping feature for every interval +flash Fast Length Adjustment of SHort reads +flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification +flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. +flux Using the black forest labs FLUX.1 models to generate image based on user input. +flye Assembly of long and error-prone reads. +footprint Find transcription factor footprints +format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file +format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels +fraggenescan Tool for finding (fragmented) genes in short read +fragpipe Data analysis for mass spectrometry-based proteomics. +free_energy Free energy tools of BRIDGE. +freebayes Galaxy Freebayes Bayesian genetic variant detector tool +freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. +freyja lineage abundances estimation +frogs Suite for metabarcoding analysis +fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. +fromgtfTobed12 Convert GTF files to BED12 format +fsd Tool that plots a histogram of sizes of read families +funannotate Funannotate is a genome prediction, annotation, and comparison software package. +garnett De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 +gatk4 Find somatic variations +gatk4 A Galaxy wrapper for Mutect2 from GATK +gblocks Gblocks +gc_derivatization In silico derivatization for GC. +gcms2isocor Conversion from GCMS PostRun Analysis to Isocor +gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs +gdal Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. +gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format +gecko Ungapped genome comparison +gemini GEMINI: a flexible framework for exploring genome variation +genebed_maf_to_fasta Stitch gene blocks given a set of coding exon intervals +genehunter_modscore Maximised LOD score pedigree analysis utility +geneiobio Gene.iobio is an interactive tool for variant and trio analysis. +genenotebook Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io +generate_pc_lda_matrix Generate a Matrix for using PC and LDA +genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." +genform genform: generation of molecular formulas by high-resolution MS and MS/MS data +genomad Identify virus and plasmid genomes from nucleotide sequences +genomescope Analyze unassembled short reads +genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases +genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). +getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension +get_flanks Get flanks returns flanking region/s for every gene +get_hrun Annotate indel variants with homopolymer context +get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) +get_pairs Separate paired and unpaired reads from two fastq files +get_reference_fasta Obtain reference genome sequence. +getindelrates_3way Estimate Indel Rates for 3-way alignments +getindels_2way Fetch Indels from pairwise alignments +getmlst Download MLST datasets by species from pubmlst.org +getorganelle GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. +gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format +gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. +gff3_rebase Rebase a GFF against a parent GFF (e.g. an original genome) +gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. +gffcompare_to_bed Filter and convert a gffCompare GTF to BED +gffread gffread filters and/or converts GFF3/GTF2 records +ggplot2 ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. +ggupset Create Upset Plots with ggupset +gi2taxonomy Fetch taxonomic representation +glimmer Glimmer makes gene predictions. +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) +gmaj GMAJ Multiple Alignment Viewer +gnali A tool to find nonessential, loss-of-function gene variants +goenrichment Performs GO Enrichment analysis. +goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data +gotohscan Find subsequences in db +gprofiler functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more +graph_converter Convert between different graph formats +graphclust GraphClust can be used for structural clustering of RNA sequences. +graphembed Compute a 2D embedding of a data matrix given supervised class information +graphicsmagick Contains tools based on GraphicsMagick +graphlan GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees +graphmap Mapper for long, error-prone reads. +graphprot GraphProt models binding preferences of RNA-binding proteins. +gromacs GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. +groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples +gsc_center_scale Center or scale (standardize) data +gsc_filter_cells Filter single cell RNAseq data on libray depth and number of detected genes +gsc_filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data +gsc_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations +gsc_high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation +gsc_mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data +gsc_scran_normalize Normalize raw counts using scran +gsc_signature_score Compute signature scores from single cell RNAseq data +gstf_preparation GeneSeqToFamily preparation converts data for the workflow +gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format +gtdbtk GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. +gtf-2-gene-list Utility to extract annotations from Ensembl GTF files. +gtfToBed12 Convert GTF files to BED12 format +gubbins Gubbins - bacterial recombination detection +guppy A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies +gvcftools gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. +gwastools +hamronization Convert AMR gene detection tool output to hAMRonization specification format. +hansel Heidelberg and Enteritidis SNP Elucidation +hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies +hapog Hapo-G - Haplotype-Aware Polishing of Genomes +happy A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. +hardklor Hardklör +hclust2 Plots heatmaps +hcluster_sg Hierarchically clustering on a sparse graph +hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids +heatmap2 heatmap.2 function from the R gplots package +heinz An algorithm for identification of the optimal scoring subnetwork. +helixer Gene calling with Deep Neural Networks +hess Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope +hgv_fundo FunDO human genes associated with disease terms +hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve +hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard +hicexplorer HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. +hicstuff A toolkit to generate and manipulate Hi-C matrices +hictk Convert cooler to juicebox_hic +hicup The HiCUP-Pipeline from the Bioinformatics Babraham Institute. +hifiasm A fast haplotype-resolved de novo assembler +hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. +high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps +hirondelle_crim_ogc_api_processes This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. +hisat HISAT is a fast and sensitive spliced alignment program. +hisat2 HISAT2 is a fast and sensitive spliced alignment program. +histogram Histogram of a numeric column +hivclustering Infers transmission networks from pairwise distances inferred by tn93 +hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. +hmmer3 HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). +homer HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. +homer Software for motif discovery and next generation sequencing analysis. +htseq-clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets +htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) +humann HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution +hybpiper Analyse targeted sequence capture data +hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack +hyphy Hypothesis Testing using Phylogenies +hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies +icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. +idba_ud Wrappers for the idba assembler variants. +idconvert Convert mass spectrometry identification files on linux or MacOSX +idr Galaxy wrappers for the IDR package from Nathan Boleu +idr_download Image Data Resource downloading tool +iedb_api Get epitope binding predictions from IEDB-API +illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays +image_info Extracts image metadata +image_math Process images using arithmetic expressions +image_registration_affine Intensity-based Image Registration +imagecoordinates_flipaxis Flip coordinate axes +imagej2 ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. +improviser Visualisation of PepXML files +incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server +indels_3way Fetch Indels from 3-way alignments +infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data +infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." +influx_data_manager Handling influx_si data inputs in Galaxy workflows +influx_si metabolic flux estimation based on [in]stationary labeling +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. +instagraal Large genome reassembly based on Hi-C data +instrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes +intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. +integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" +intermine_galaxy_exchange InterMine Exporter +interpolation Run IDW interpolation based on a .csv and .geojson file +interproscan Interproscan queries the interpro database and provides annotations. +intersect Intersect the intervals of two datasets +interval2maf Extract MAF blocks given a set of intervals +intervene Create pairwise and upset plots +iphop Integrated Phage Host Prediction +ipo [W4M][LC-MS] IPO +iprscan5 Interproscan queries the interpro database and provides annotations. +iqtree Efficient phylogenomic software by maximum likelihood +irissv Refine insertion sequences +isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" +isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. +isolib Create an isotopic pattern library for given compounds and adducts. +isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments +itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. +ivar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing +iwtomics Interval-Wise Testing for Omics Data +jasminesv Merge structural variants across samples +jbrowse JBrowse Genome Browser integrated as a Galaxy Tool +jbrowse A tool allowing to export a JBrowse dataset into a JBrowse docker container +jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool +jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) +jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA +join Join the intervals of two datasets side-by-side +join_files_by_id This tool will join datasets according to a column with identifier +join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. +jq JQ is a lightweight and flexible command-line JSON processor +jupyter_job Run jupyter notebook script in Galaxy +justdiff Unix diff +justgzip Compress fastq sequence files +jvarkit Jvarkit : Java utilities for Bioinformatics +kallisto kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. +kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. +kat_filter Filtering kmers or reads from a database of kmers hashes +kat_sect SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. +kc-align Kc-Align custom tool +kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. +kernel_canonical_correlation_analysis Kernel Canonical Correlation Analysis +kernel_principal_component_analysis Kernel Principal Component Analysis +khmer In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more +king Kinship-based INference for Gwas +kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. +kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) +kma Map with KMA +kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file +kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model +kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. +kraken2 Kraken2 for taxonomic designation. +kraken2tax Convert Kraken output to Galaxy taxonomy data. +kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) +kraken_taxonomy_report Kraken taxonomy report +krakentools KrakenTools is a suite of scripts to be used alongside the Kraken +krocus Predict MLST directly from uncorrected long reads +label_to_binary Convert label map to binary image +labelimage2points Label Image to Points +labels remaps and annotates alignments +landmark_registration Landmark Registration +last LAST finds similar regions between sequences. +lastz Galaxy wrappers for the Lastz and Lastz_d +lastz_paired_reads Galaxy wrapper for the Lastz alignment tool on paired reads +lca_wrapper Find lowest diagnostic rank +lcrgenie Ligase Chain Reaction Genie +lda_analysis Perform Linear Discriminant Analysis +legsta Performs in silico Legionella pneumophila sequence based typing. +length_and_gc_content Gets gene length and gc content from a fasta and a GTF file +lfq_protein_quant Enable protein summarisation and quantitation +lighter Lighter is a kmer-based error correction method for whole genome sequencing data +limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline +lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) +linear_regression Perform Linear Regression +links Scaffold genome assemblies with long reads. +locarna LocARNA - A suite for multiple alignment and folding of RNAs +lofreq LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. +logistic_regression_vif Perform Logistic Regression with vif +logol Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence +longorf obtain longest ORF in six-frame translations +lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) +lotus2 LotuS2 OTU processing pipeline +ltq_iquant_cli +lumpy_smoove Galaxy wrapper of the lumpy-using smoove workflow +lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery +lumpy_sv Find structural variations +m6anet m6anet to detect m6A RNA modifications from nanopore data +maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. +macs2 MACS - Model-based Analysis of ChIP-Seq +maf_cpg_filter Mask CpG/non-CpG sites from MAF file +maf_stats MAF Coverage statistics +mafft Multiple alignment program for amino acid or nucleotide sequences +maftoaxt Convert dataset from MAF to axt format +mageck Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. +mahotas_features Compute image features using mahotas. +make_data_paper_sketches This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. +make_nr Make a FASTA file non-redundant +maker MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. +maldiquant MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. +malt Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. +manta Structural variant and indel caller for mapped sequencing data +map_param_value Map a parameter value to another value +map_peptides_to_bed Map peptides to a reference genome for display by a genome browser +mapping_quality_stats Collects and shows the distribution of MAPQ values in a BAM alignment file +mapping_to_ucsc Format mapping data as UCSC custom track +mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. +marine_omics The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data +mash Fast genome and metagenome distance estimation using MinHash +mashmap Fast local alignment boundaries +masigpro Identify significantly differential expression profiles in time-course microarray experiments +matchms Searching, filtering and converting mass spectral libraries. +mauve_contig_mover Order a draft genome relative to a related reference genome +mavedb data source for MaveDB +maxbin2 clusters metagenomic contigs into bins +maxquant wrapper for MaxQuant +mcl The Markov Cluster Algorithm, a cluster algorithm for graphs +mdanalysis MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations +mdfileconverter A tool for interconverting between different MD structure and trajectory file formats. +mdslicer A tool for slicing trajectory files using MDTraj. +mdtraj MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories +mea Maximum expected accuracy prediction +mean-per-zone Creates a png image showing statistic over areas as defined in the vector file +measure_gastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index +medaka Sequence correction provided by ONT Research +medenv Retrieve environmental data from etopo, cmems and woa +megablast_xml_parser Parse blast XML output +megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. +megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) +megan MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). +meme The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. +meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. +meneco Meneco computes minimal completions to your draft network with reactions from a repair network +meningotype Assign sequence type to N. meningitidis genome assemblies +merge Merge the overlapping intervals of a dataset +merge_cols Merge columns together. +mergeneighboursinlabelimage Merge Neighbours in Label Image +merlin Pedigree Analysis package +merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. +meryl Meryl a k-mer counter. +meta_proteome_analyzer MetaProteomeAnalyzer +metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. +metabuli Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences +metaeuk MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. +metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage +metagenomeseq metagenomeSeq Normalization +metanovo Produce targeted databases for mass spectrometry analysis. +metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis +metaquantome quantitative analysis of microbiome taxonomy and function +metawrapmg A flexible pipeline for genome-resolved metagenomic data analysis +metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) +metfrag-vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag +methtools tools for methylation analysis +methyldackel A tool for processing bisulfite sequencing alignments +methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. +metilene Differential DNA methylation calling +mfassignr The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements +mg_toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. +mgf_formatter +mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. +miclip Identification of binding sites in CLIP-Seq data. +microsatbed Select microsatellites for a bed file +microsatellite_birthdeath Identify microsatellite births and deaths +microsats_alignment_level Extract Orthologous Microsatellites from pair-wise alignments +microsats_mutability Estimate microsatellite mutability by specified attributes +migmap mapper for full-length T- and B-cell repertoire sequencing +minced MinCED - Mining CRISPRs in Environmental Datasets +mine Maximal Information-based Nonparametric Exploration +minia Short-read assembler based on a de Bruijn graph +miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) +minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences +minipolish Polishing miniasm assemblies +miniprot Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. +miranda Finds potential target sites for miRNAs in genomic sequences +miranda2asko Converts miRanda output into AskOmics format +mircounts Generates miRNA count lists from read alignments to mirBase. +mirmachine Tool to detect miRNA in genome sequences +mirnature Computational detection of canonical microRNAs +misc +mitobim assemble mitochondrial genomes +mitohifi Assembly mitogenomes from Pacbio HiFi read. +mitos de-novo annotation of metazoan mitochondrial genomes +mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model +mlst Scan contig files against PubMLST typing schemes +moFF moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. +moabs MOABS for differential methylation analysis on Bisulfite sequencing data. +mob_suite MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies +molecule2gspan converter +monocle3 De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. +morpheus Morpheus MS Search Application +morphological_operations Apply morphological operations to images +mosdepth fast and flexible BAM/CRAM depth calculation +mothur Mothur wrappers +motus Tool for profiling the abundance of microbial taxa. +mqc Ribosome profiling mapping quality control tool +mqppep MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA +mrbayes A program for the Bayesian estimation of phylogeny. +ms2deepscore Mass spectra similarity scoring using a trained ms2deepscore model. +ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. +msPurity [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data +msaboot A multiple sequences alignment bootstrapping tool. +msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container +msgfplus MSGF+ +msmetaenhancer +msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. +msp_merge +msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data +msstats MSstats tool for analyzing mass spectrometry proteomic datasets +msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling +mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome +multigps Analyzes collections of multi-condition ChIP-seq data. +multigsea GSEA-based pathway enrichment analysis for multi-omics data +multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report +multispecies_orthologous_microsats Extract orthologous microsatellites +mummer Draw dotplots using mummer, mucmer, or promer with mummerplot +mummer4 Mummer4 Tools +music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) +mutate_snp_codon Mutate Codons with SNPs +mutational_patterns Mutational patterns and signatures in base substitution catalogs +mykrobe Antibiotic resistance predictions +mykrobe_parser RScript to parse the results of mykrobe predictor. +mz_to_sqlite Creates a SQLite database for proteomics data +mzmine mass-spectrometry data processing, with the main focus on LC-MS data +mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. +mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML +naltorfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) +nanocompore Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. +nanoplot Plotting tool for long read sequencing data and alignments +nanopolish Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. +nanopolishcomp NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. +nastiseq A method to identify cis-NATs using ssRNA-seq +ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API +ncbi_blast_plus NCBI BLAST+ +ncbi_datasets NCBI datasets downloads biological sequence data across all domains of life from NCBI. +ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) +ncbi_entrez_direct NCBI Entrez Direct allow fetching data from NCBI Databases +ncbi_entrez_eutils NCBI Entrez E-Utilties allow fetching data from NCBI Databases +ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. +ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). +necat Error correction and de-novo assembly for ONT Nanopore reads +netboxr netboxr enables automated discovery of biological process modules by network analysis +newick_utils Perform operations on Newick trees +nextclade Identify differences between your sequences and a reference sequence used by Nextstrain +nextdenovo String graph-based de novo assembler for long reads +ngmlr CoNvex Gap-cost alignMents for Long Reads +ngsutils NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. +nlstradamus Find nuclear localization signals (NLSs) in protein sequences +nmr_annotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation +nmr_annotation2d [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra +nmr_preprocessing [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction +nonpareil Estimate average coverage in metagenomic datasets +normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data +novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. +nucleosome_prediction Prediction of Nucleosomes Positions on the Genome +nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. +numeric_clustering Clustering tool for numberic values +oases Short read assembler +obisindicators Compute biodiveristy indicators for marine data from obis +obitools OBITools is a set of programs developed to simplify the manipulation of sequence files +ocean Access, process, visualise oceanographic data for the Earth System +ococo Variant detection of SNVs +odgi Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. +ogcProcess_otb_bandmath Outputs a monoband image which is the result of a mathematical operation on several multi-band images. +ogcProcess_otb_meanShiftSmoothing This application smooths an image using the MeanShift algorithm. +omark Proteome quality assessment software +omero Import images, region of interest, metadata into an OMERO.server using omero-py +omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down +omero_get_children_ids Get omero id of children of an omero object id +omero_get_full_images Get full images from omero +omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels +omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements +ont_fast5_api ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. +onto_toolkit ONTO-Toolkit is a collection of tools for managing ontologies. +openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." +openmm OpenMM is a toolkit for molecular simulation using high performance GPU code. +openms OpenMS Suite for LC/MS data management and analyses +openms OpenMS in version 2.1. +optdoe Optimal Design Of Experiment +optitype Precision HLA typing from NGS data +orfipy Galaxy wrapper for ORFIPY +orientationpy Compute image orientation +orthofinder Accurate inference of orthologous gene groups made easy +overlay_images Overlay two images +packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection +packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations +pacu PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. +pairtools Flexible tools for Hi-C data processing +pandas_rolling_window Rolling window calculations +pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. +pangolin Phylogenetic Assignment of Named Global Outbreak LINeages +paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. +parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. +partialr_square Compute partial R square +pathifier pathifier +pathview Pathview is a tool set for pathway based data integration and visualization. +pathwaymatcher Reactome Pathway Matcher +patrist Extract Patristic Distance From a Tree +pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference +pbmm2 A minimap2 SMRT wrapper for PacBio data. +pbtk Convert PacBio Bam File to fasta or fastq file +pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. +peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data +peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. +pear PEAR evaluates all possible paired-end read overlaps +pearson_correlation Pearson and apos Correlation between any two numeric columns +pep_pointer PepPointer categorizes peptides by their genomic coordinates. +pepquery A peptide-centric MS search engine for novel peptide identification and validation. +pepquery2 PepQuery2 peptide-centric MS search for peptide identification and validation +peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files +peptideshaker PeptideShaker and SearchGUI +peptimapper Proteogenomics workflow for the expert annotation of eukaryotic genomes +pepxml_to_xls Convert PepXML to Tabular +percolator Percolator +perf suitable for boolean classification problems +permutate_axis Permutates axes +pfamscan Search a FASTA sequence against a library of Pfam HMM. +pg_tools tool suite for dealing with Postgresql databases from Galaxy's history +pgsnp2gd_snp Convert from pgSnp to gd_snp +pharmcat Pharmacogenomics Clinical Annotation Tool +pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes +phyloseq Handling and analysis of high-throughput microbiome census data +phyml PhyML is a phylogeny software based on the maximum-likelihood principle. +physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes +physiofit_manager Handling of physiofit input files +pi_db_tools HiRIEF tools +picard Picard SAM/BAM manipulation tools. +pick_value Compose a text parameter value using text, integer and float values +picrust PICRUSt wrappers +picrust2 PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States +pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases +pileup_parser Filter pileup on coverage and SNPs +pilon pilon is a tool for assembly improvement and variant analysis in bacteria +pindel Pindel detects genome-wide structural variation. +pipelign Multipe sequence alignment +pipmir A method to identify novel plant miRNA. +piranha Piranha is a peak-caller for CLIP- and RIP-Seq data +pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. +plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images +plasflow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. +plasmid_profiler Explores plasmid content in WGS data +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler +plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" +plasmidspades Genome assembler for assemblying plasmid +platypus efficient and accurate variant-detection in high-throughput sequencing data +plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. +plot_from_lda "Draw ROC plot on ""Perform LDA"" output" +plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. +plotly_ml_performance_plots performance plots for machine learning problems +plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly +plotly_regression_performance_plots performance plots for regression problems +pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS +pneumocat Pneumococcal Capsular Typing of illumina fastq reads +points2labelimage Points to label image +points_association_nn Association of points in consecutive frames +poisson2test Poisson two-sample test +polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" +porechop Porechop - Finding and removing adapters from Oxford Nanopore reads +poretools A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. +positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. +positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. +predictnls Python reimplementation of predictNLS for Galaxy +presto pRESTO toolkit for immune repertoire analysis. +pretext Process genome contacts maps processing images. +principal_component_analysis Principal Component Analysis +prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets +probecoverage computes and plots read coverage of genomic regions by sequencing datasets +prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes +progressivemauve Mauve/ProgressiveMauve Multiple Sequence Aligner +projective_transformation Projective transformation +projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates +prokka Rapid annotation of prokaryotic genomes +promer Aligns two sets of contigs and reports amino acid substitutions between them +prot-scriber Protein annotation of short human readable descriptions +protease_prediction This tool can learn the cleavage specificity of a given class of proteases. +protein_analysis TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb +protein_properties Calculation of various properties from given protein sequences +proteinortho Proteinortho is a tool to detect orthologous proteins/genes within different species. +proteinpilot +proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. +proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. +proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. +proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. +proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. +proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. +proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. +proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. +proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. +proteore_venn_diagram ProteoRE JVenn Diagram +protxml_to_xls +pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. +psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. +psm2sam PSM to SAM +psm_eval +psm_validation Validate PSM from Ion Fragmentation +psy-maps Visualization of regular geographical data on a map with psyplot +pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data +purge_dups Purge haplotigs and overlaps in an assembly based on read depth +pycoqc QC metrics for ONT Basecalling +pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. +pygenometracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. +pyprophet Semi-supervised learning and scoring of OpenSWATH results. +pyscenic PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ +pysradb pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. +pyteomics Tools using the pyteomics library +pyvo_integration Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy +qcxms QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). +qfilt Filter sequencing data +qiime_add_on QIIME to perform microbial community analysis +qiime_core QIIME to perform microbial community analysis +qiime_extract_viz Extract vizualization from QIIME artifacts +qq_tools +qualimap Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. +quality_filter Filter nucleotides based on quality scores +quantp Correlation between protein and transcript abundance +quantwiz_iq Isobaric Quantitation using QuantWiz-IQ +quasitools A collection of tools for analysing Viral Quasispecies +quast Quast (Quality ASsessment Tool) evaluates genome assemblies. +query Execute an SQL statement on a set of tables +query_impc Contains a tool to query the IMPC database. +query_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output +quickmerge Merge long-read and hybrid assemblies to increase contiguity +qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type +rRNA Identification of ribosomal RNA genes in metagenomic fragments. +raceid RaceID3, StemID2, FateID - scRNA analysis +racon Consensus module for raw de novo DNA assembly of long uncorrected reads. +ragtag Reference-guided scaffolding of draft genomes tool. +ramclustr +rapidnj Galaxy wrapper for the RapidNJ tool +rasusa Randomly subsample sequencing reads to a specified coverage +raven Raven is a de novo genome assembler for long uncorrected reads. +rawtools Raw Tools +raxml RAxML - A Maximum Likelihood based phylogenetic inference +rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs +rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments +rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. +rcve Compute RCVE +rcx-tk Tools to process metadata or alkane files. +rdock Docking ligands to proteins and nucleic acids +read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads +reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. +recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" +recetox_aplcms Peak detection tool for HRMS profile data. +recetox_msfinder +recetox_xmsannotator +red Red (REpeat Detector) +refseq_masher Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. +regex_find_replace Use python regular expressions to find and replace text +regionalgam +rem_complex Removes molecular coordination complexes. +remove_beginning Remove lines from the beginning of a file. +remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation +rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results +repeat_channels Convert single-channel to multi-channel image +repeat_masker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. +repeatexplorer2 Tool for annotation of repeats from unassembled shotgun reads. +repeatmasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. +repeatmodeler RepeatModeler - Model repetitive DNA +repenrich Repeat element profiling +repenrich2 Repeat element profiling using bowtie2 aligner +replaceColumn A tool to replace all column entries of a file given by values of a key-value file. +replace_chromosome_names Replace chromosome names +repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. +reshape2 Flexibly restructure and aggregate data using just the two functions melt and dcast +resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. +rest_tool This tool fetches data from pubchem via the PubChem REST API. +retip +retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers +retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format +revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. +revoluzer revoluzer wrappers +rfove Perform segmentation region-based fitting of overlapping ellipses +rgcca multi-block analysis +rgrnastar RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper +riassigner +ribotaper A method for defining traslated ORFs using Ribosome Profiling data. +ribowaltz Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data +rmap RMAP for Solexa Short Reads Alignment +rmapq RMAPQ for Solexa Short Reads Alignment with Quality Scores +rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. +rna_shapes Compute secondary structures of RNA +rnabob Fast pattern searching for RNA structural motifs +rnacode Analyze the protein coding potential in MSA +rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. +rnaformer RNAformer: RNA secondary structure prediction +rnalien RNAlien unsupervized RNA family model construction +rnaquast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. +rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs +rnaz RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. +roary Roary the pangenome pipeline +rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output +rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 +rpbasicdesign Extracting enzyme IDs from rpSBML files +rpfba Perform FBA for the RetroPath2.0 heterologous pathways +rptools Suite of tools that work on rpSBML format +rrparser Reaction Rules Parser +rsat_filter_snps Filter SNPs in RSAT Matrix Scan output +rsem transcript quantification from RNA-Seq data +rseqc an RNA-seq quality control package +ruvseq Remove Unwanted Variation from RNA-Seq Data +sailfish Sailfish is a tool for transcript quantification from RNA-seq data +salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. +salmon-kallisto-mtx-to-10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data +salsa2 A tool to scaffold long read assemblies with Hi-C +sam2interval Convert SAM to interval. +sam_bitwise_flag_filter Filter SAM on bitwise flag values +sambamba filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM +sambamba Sambamba: process your BAM data faster! +samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files +sample_seqs Sub-sample sequences files (e.g. to reduce coverage) +samtools +samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) +samtools_depth Coverage depth via samtools +samtools_idxstats BAM mapping statistics (using samtools idxstats) +sansa Sansa is a tool for structural variant annotation. +sarscov2formatter sarscov2formatter custom script +sarscov2summary sarscov2summary custom script +sashimi_plot Generates a sashimi plot from bam files. +sbml2sbol Convert SBML to SBOL format +sc3 De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. +scaffold +scale_image Scale image +scanpy Scanpy – Single-Cell Analysis in Python +scanpy scanpy-scripts, command-line wrapper scripts around Scanpy. +scater Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. +scater De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. +scatterplot Scatterplot of two numeric columns +sccaf SCCAF: Single Cell Clustering Assessment Framework. +sceasy Convert scRNA data object between popular formats +sceasy Converter between difference single-cell formats +schicexplorer scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. +scikit-bio scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics +scmap De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. +scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. +scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data +scpred De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 +scripting suite_scripting +sdmpredictors Terrestrial and marine predictors for species distribution modelling. +seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. +sed Manipulate your data with the sed command line tool. +segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. +segemehl segemehl - short read mapping with gaps +segmetrics Image segmentation and object detection performance measures +selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format +selenzy_wrapper Performs enzyme selection from a reaction query. +semibin SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks +seq2hla Precision HLA typing and expression from RNAseq data +seq_composition Sequence composition +seq_filter_by_id Filter sequences by ID +seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files +seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) +seq_primer_clip Trim off 5' or 3' primers +seq_rename Rename sequences with ID mapping from a tabular file +seq_select_by_id Select sequences by ID +seqcomplexity Sequence complexity for raw reads +seqkit A cross-platform and ultrafast toolkit for FASTA/Q file manipulation +seqprep Tool for merging paired-end Illumina reads and trimming adapters. +seqsero2 Salmonella serotype prediction from genome sequencing data +seqtk Toolkit for processing sequences in FASTA/Q formats +seqtk_nml Tool to downsample fastq reads +sequence_format_converter various fasta to tabular conversions +seqwish Alignment to variation graph inducer +seurat De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 +seurat Seurat - R toolkit for single cell genomics +sgwb SGWB +shasta Fast de novo assembly of long read sequencing data +shift-longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees +shorah Reconstruct haplotypes using ShoRAH in amplicon mode +short_reads_figure_high_quality_length Histogram of high quality score reads +short_reads_figure_score Build base quality distribution +short_reads_trim_seq Select high quality segments +shovill Faster de novo assembly pipeline based around Spades +show_beginning Select lines from the beginning of a file. +show_tail Select lines from the end of a file. +sicer Statistical approach for the Identification of ChIP-Enriched Regions +sickle A windowed adaptive trimming tool for FASTQ files using quality +simtext A text mining framework for interactive analysis and visualization of similarities among biomedical entities. +sina SINA reference based multiple sequence alignment +sinto Sinto single-cell analysis tools +sistr_cmd SISTR in silico serotyping tool +sixgill Six-frame Genome-Inferred Libraries for LC-MS/MS +sklearn Machine Learning tool suite from Scikit-learn +skyline2isocor Converting skyline output to IsoCor input +slamdunk Slamdunk maps and quantifies SLAMseq reads +sleuth Sleuth is a program for differential analysis of RNA-Seq data. +slice_image Slice image +small_rna_clusters clusters small rna reads in alignment BAM files +small_rna_maps Generates small read maps from alignment BAM files +small_rna_signatures Computes the tendency of small RNAs to overlap with each other. +smallgenomeutilities Set of utilities for manipulating small viral genome data. +smalt SMALT aligns DNA sequencing reads with a reference genome. +smart_domains SMART domains +smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization +smithsonian-volcanoes Retrieve data from Volcanoes of the World (VOTW) Database +smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing +snap SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +snapatac2 SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis +sniffles Galaxy wrapper for sniffles +snipit Summarise snps relative to a reference sequence +snippy Contains the snippy tool for characterising microbial snps +snp-dists Compute pairwise SNP distance matrix from a FASTA sequence alignment +snp-sites Finds SNP sites from a multi-FASTA alignment file +snpeff SnpEff is a genetic variant annotation and effect prediction toolbox +snpeff-covid19 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox +snpfreq snpFreq significant SNPs in case-control data +snpfreqplot A plotting app to visualise the SNPs across a region +snpsift snpEff SnpSift tools from Pablo Cingolani +snpsift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani +snpsift_genesets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome +snv_matrix Generate matrix of SNV distances +snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza +socru Order and orientation of complete bacterial genomes +sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. +sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. +spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. +spades_header_fixer Fixes Spades Fasta ids +spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. +spapros Select and evaluate probe sets for targeted spatial transcriptomics. +spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. +spec2vec Mass spectra similarity scoring using a trained Spec2Vec model. +spectrast2spectrast_irt Filter from spectraST files to swath input files +spectrast2tsv Filter from spectraST files to swath input files +split_file_on_column Split a file on a specific column. +split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. +split_labelmap Split Labelmaps +split_paired_reads Split paired end reads +splitfasta Split a multi-sequence fasta file into files containing single sequences +spocc Get species occurences data +spolpred A program for predicting the spoligotype from raw sequence reads +spot_detection_2d Spot detection in 2D image sequence +spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads +spyboat Wavelet analysis for 3d-image stacks +sr_bowtie bowtie wrapper tool to align small RNA sequencing reads +sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. +sra-tools NCBI Sequence Read Archive toolkit utilities +srs_tools Compute biodiversity indicators for remote sensing data from Sentinel 2 +srst2 Short Read Sequence Typing for Bacterial Pathogens +srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens +sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data +stacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq +stacks2 Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq +star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR +staramr Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. +statistics Tool for computing statistical tests. +stoc Tools to analyse STOC data. +straindesign Toolbox to optimize biological model +strelka Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. +stress_ng stress test a computer system in various selectable ways +stringmlst Rapid and accurate identification of the sequence type (ST) +stringtie StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. +structure for using multi-locus genotype data to investigate population structure. +structureharvester for parsing STRUCTURE outputs and for performing the Evanno method +substitution_rates Estimate substitution rates for non-coding regions +substitutions Fetch substitutions from pairwise alignments +subtract Subtract the intervals of two datasets +subtract_query Subtract Whole Dataset from another dataset +suite_qiime2__alignment +suite_qiime2__composition +suite_qiime2__cutadapt +suite_qiime2__dada2 +suite_qiime2__deblur +suite_qiime2__demux +suite_qiime2__diversity +suite_qiime2__diversity_lib +suite_qiime2__emperor +suite_qiime2__feature_classifier +suite_qiime2__feature_table +suite_qiime2__fragment_insertion +suite_qiime2__longitudinal +suite_qiime2__metadata +suite_qiime2__phylogeny +suite_qiime2__quality_control +suite_qiime2__quality_filter +suite_qiime2__rescript +suite_qiime2__sample_classifier +suite_qiime2__taxa +suite_qiime2__vsearch +suite_qiime2_core +suite_qiime2_core__tools +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl +superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images +swift Parallel MCMC Linkage Analysis +syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. +t2ps Draw phylogeny +t2t_report Summarize taxonomy +t_coffee T-Coffee +t_test_two_samples T Test for Two Samples +table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered +table_compute Perform general-purpose table operations +tables_arithmetic_operations Arithmetic Operations on tables +tabular_to_fasta Tabular-to-FASTA +tabular_to_fastq Tabular to FASTQ converter +tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. +tapscan Search for transcription associated proteins (TAPs) +tarfast5 produces a tar.gz archive of fast5 sequence files +targetfinder Plant small RNA target prediction tool +tasmanian_mismatch Analysis of positional mismatches +taxonkit TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit +taxonomy_filter_refseq Filter RefSeq by taxonomy +taxonomy_krona_chart Krona pie chart from taxonomic profile +taxpasta standardise taxonomic profiles +tb-profiler Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. +tb_variant_filter M. tuberculosis H37Rv VCF filter +tbl2gff3 Table to GFF3 +tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) +te_finder Transposable element insertions finder +telescope Single locus resolution of Transposable ELEment expression. +tetoolkit The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. +tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. +text_processing High performance text processing tools using the GNU coreutils, sed, awk and friends. +tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. +tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. +tn93 Compute distances between sequences +tool_recommendation_model Create model to recommend tools +tooldistillator ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files +tophat Tophat for Illumina +tophat2 Tophat - fast splice junction mapper for RNA-Seq reads +tophat_fusion_post Wrapper for Tophat-Fusion post step +topologyeditors Set of python scripts and associated tool files that can be used to modify topology files. +tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. +tracy +transdecoder TransDecoder finds coding regions within transcripts +transit TRANSIT +translate_bed Translate BED transcript CDS or cDNA in 3 frames +translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column +transtermhp Finds rho-independent transcription terminators in bacterial genomes +tree_relabeler Relabels the tips of a newick formatted tree. +trim_galore Trim Galore adaptive quality and adapter trimmer +trimmer Trim leading or trailing characters. +trimmomatic A flexible read trimming tool for Illumina NGS data +trinity Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq +trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. +tripal Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal +trna_prediction Aragorn predicts tRNA and tmRNA in nucleotide sequences. +trycycler Trycycler toolkit wrappers +tsebra This tool has been developed to combine BRAKER predictions. +tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation +twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA +tximport Wrapper for the Bioconductor package tximport +ucsc-cell-browser Python pipeline and Javascript scatter plot library for single-cell datasets +ucsc_axtchain Chain together genome alignments +ucsc_axttomaf Convert dataset from axt to MAF format. +ucsc_blat Standalone blat sequence search command line tool +ucsc_chainnet Make alignment nets out of chains +ucsc_chainprenet Remove chains that don't have a chance of being netted +ucsc_chainsort Sort chains. By default sorts by score. +ucsc_custom_track Build custom track for UCSC genome browser +ucsc_netfilter Filter out parts of net +ucsc_netsyntenic Add synteny info to a net dataset +ucsc_nettoaxt Convert net (and chain) to axt format. +umi_tools UMI-tools extract - Extract UMIs from fastq +unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. +unipept Unipept retrieves metaproteomics information +uniprot_rest_interface UniProt ID mapping and sequence retrieval +uniprotxml_downloader Download UniProt proteome in XML or fasta format +unzip Unzip file +upload_roi_and_measures_to_omero Upload the ROI coordinates and the measurements to the omero server +usher UShER toolkit wrappers +valet A pipeline for detecting mis-assemblies in metagenomic assemblies. +validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. +vapor Classify Influenza samples from raw short read sequence data +vardict VarDict - calls SNVs and indels for tumour-normal pairs +variant_analyzer Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data +varscan VarScan is a variant caller for high-throughput sequencing data +varscan_vaf Compute variant allele frequency in vcf files generated by varscan. +varscan_version_2 VarScan wrapper +varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses +vcf2maf vcf2maf: Convert VCF into MAF +vcf2pgsnp VCF to pgSnp +vcf2snvalignment Generates multiple alignment of variant calls +vcf2tsv Converts VCF files into tab-delimited format +vcf_annotate Annotate a VCF file (dbSNP, hapmap) +vcf_extract Extract reads from a specified region +vcf_filter Filter a VCF file +vcf_intersect Generate the intersection of two VCF files +vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. +vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines +vcfanno Annotate VCF files +vcfannotate Intersect VCF records with BED annotations +vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. +vcfbedintersect Intersect VCF and BED datasets +vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record +vcfcheck Verify that the reference allele matches the reference genome +vcfcombine Combine multiple VCF datasets +vcfcommonsamples Output records belonging to samples commong between two datasets. +vcfdistance Calculate distance to the nearest variant. +vcffilter Tool for filtering VCF files +vcffixup Count the allele frequencies across alleles present in each record in the VCF file. +vcfflatten Removes multi-allelic sites by picking the most common alternate +vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles +vcfgenotypes Convert numerical representation of genotypes to allelic. +vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. +vcfleftalign Left-align indels and complex variants in VCF dataset +vcfprimers Extract flanking sequences for each VCF record +vcfrandomsample Randomly sample sites from VCF dataset +vcfselectsamples Select samples from a VCF file +vcfsort Sort VCF dataset by coordinate +vcftools_annotate Annotate VCF using custom/user-defined annotations +vcftools_compare Compare VCF files to get overlap and uniqueness statistics +vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence +vcftools_isec Intersect multiple VCF datasets +vcftools_merge Merge multiple VCF datasets into a single dataset +vcftools_slice Subset VCF dataset by genomic regions +vcftools_subset Select samples from a VCF dataset +vcfvcfintersect Intersect two VCF datasets +vegan an R package fo community ecologist +velocyto Velocyto is a library for the analysis of RNA velocity. +velvet de novo genomic assembler specially designed for short read sequencing technologies +velvet_optimiser Automatically optimize Velvet assemblies +venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc +verify_map Checks the mapping quality of all BAM(s) +verkko Telomere-to-telomere assembly pipeline +vg Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods +vibrant Virus Identification By iteRative ANnoTation +vienna_rna ViennaRNA - Prediction and comparison of RNA secondary structures +vigiechiro Tools created by the vigiechiro team to analyses and identify chiro sounds files. +virAnnot virAnnot wrappers +virheat generates a heatmap of allele frequencies from vcf files +virhunter Deep Learning method for novel virus detection in sequencing data +virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. +visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool +vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations +volcanoplot Tool to create a Volcano Plot +voronoi_tessellation Compute Voronoi tesselation +vsearch VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. +vsnp The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. +vt A tool set for short variant discovery in genetic sequence data. +w4mclassfilter Filter W4M data by values or metadata +w4mconcatenate [W4M][Utils] concatenate two Metadata tables +w4mcorcov OPLS-DA Contrasts of Univariate Results +w4mjoinpn Join positive- and negative-mode W4M datasets +wade identify regions of interest +waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. +weather_app provides simple weather in text format +weblogo3 Sequence Logo generator for fasta +weightedaverage Assign weighted-average of the values of features overlapping an interval +whisper Transcribe audio or video files to text using the OpenAI Whisper. +wigtobigwig converts bedGraph (wig) files into binary bigwig +windowmasker Identify repetitive regions using WindowMasker +windowsplitter Make windows +winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. +woundhealing Tool to automate quantification of wound healing in high-throughput microscopy scratch assays +wsi_extract_top_view WSI Extract Top View +wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. +xarray xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. +xcms +xmlstarlet Tool to convert a xml file from one metadata standard to another +xpath XPath XML querying tool +xpore Identification and quantification of differential RNA modifications from direct RNA sequencing +xtb Performs semiempirical molecular optimization. +xy_plot Plotting tool for multiple series and graph types +yac_clipper Clips 3' adapters for small RNA sequencing reads. +yahs Yet Another Hi-C scaffolding tool +zeiss_lmd_converter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems +zerone ChIP-seq discretization and quality control +zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. diff --git a/communities/imaging/metadata/tool_status.tsv b/communities/imaging/metadata/tool_status.tsv deleted file mode 100644 index e69de29b..00000000 diff --git a/communities/imaging/resources/tools.tsv b/communities/imaging/resources/tools.tsv deleted file mode 100644 index 52c61212..00000000 --- a/communities/imaging/resources/tools.tsv +++ /dev/null @@ -1,68 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. 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Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 False -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 False -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 False -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 False -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 False -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 False -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 False +Galaxy wrapper id Description To keep Deprecated +2d_auto_threshold Automatic thresholding +2d_feature_extraction 2D feature extraction +2d_filter_segmentation_by_features filter segmentation by rules +2d_histogram_equalization 2d histogram equalization +2d_simple_filter 2d simple filter +anisotropic_diffusion Anisotropic image diffusion +background_removal Background removal filters using scikit-image +bfconvert Convert image +bia-ftplinks Tool to query ftp links for study from bioimage archive +binary2labelimage Binary 2 label image +binaryimage2points Binary Image to Points +bioformats2raw Convert image to OME-Zarr +bioimaging Load model from BioImage.IO and make inferences +cellpose Cellpose is an anatomical segmentation algorithm +cellprofiler cellProfiler wrapper +cellprofiler_v4 cellProfiler4 wrapper +color_deconvolution Color-deconvolution methods +colorize_labels Colorize label map +concat_channels Concatenate images +coordinates_of_roi Coordinates of ROI +count_objects Count Objects +curve_fitting Polynomial curve fitting to data points +detection_viz Detection Visualization +graphicsmagick Contains tools based on GraphicsMagick +hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack +image_info Extracts image metadata +image_math Process images using arithmetic expressions +image_registration_affine Intensity-based Image Registration +imagecoordinates_flipaxis Flip coordinate axes +imagej2 ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. +incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server +label_to_binary Convert label map to binary image +labelimage2points Label Image to Points +landmark_registration Landmark Registration +mahotas_features Compute image features using mahotas. +measure_gastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index +mergeneighboursinlabelimage Merge Neighbours in Label Image +morphological_operations Apply morphological operations to images +omero Import images, region of interest, metadata into an OMERO.server using omero-py +omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down +omero_get_children_ids Get omero id of children of an omero object id +omero_get_full_images Get full images from omero +omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels +omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements +orientationpy Compute image orientation +overlay_images Overlay two images +permutate_axis Permutates axes +plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images +points2labelimage Points to label image +points_association_nn Association of points in consecutive frames +projective_transformation Projective transformation +projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates +qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type +repeat_channels Convert single-channel to multi-channel image +rfove Perform segmentation region-based fitting of overlapping ellipses +scale_image Scale image +segmetrics Image segmentation and object detection performance measures +slice_image Slice image +split_labelmap Split Labelmaps +spot_detection_2d Spot detection in 2D image sequence +spyboat Wavelet analysis for 3d-image stacks +superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images +upload_roi_and_measures_to_omero Upload the ROI coordinates and the measurements to the omero server +visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool +voronoi_tessellation Compute Voronoi tesselation +woundhealing Tool to automate quantification of wound healing in high-throughput microscopy scratch assays +wsi_extract_top_view WSI Extract Top View diff --git a/communities/machine-learning/metadata/tool_status.tsv b/communities/machine-learning/metadata/tool_status.tsv index 107c021b..940318d5 100644 --- a/communities/machine-learning/metadata/tool_status.tsv +++ b/communities/machine-learning/metadata/tool_status.tsv @@ -1 +1,2 @@ + To keep Deprecated jupyter_job FALSE FALSE \ No newline at end of file diff --git a/communities/machine-learning/resources/tools.tsv b/communities/machine-learning/resources/tools.tsv deleted file mode 100644 index c906ccd5..00000000 --- a/communities/machine-learning/resources/tools.tsv +++ /dev/null @@ -1,13 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 False -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 False -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 False -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. 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More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. 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To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. 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Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 True False False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 False -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 False +Galaxy wrapper id Description To keep Deprecated +biomodelsML Wrappers for tools to bring BioModels AI models into Galaxy. +chatgpt Using the OpenAI GPT models to generate text based on user input. +chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing +decontaminator Deep Learning method for novel virus detection in sequencing data +deepmicro Representation learning and classification framework +flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. +flux Using the black forest labs FLUX.1 models to generate image based on user input. +jupyter_job Run jupyter notebook script in Galaxy False False +sklearn Machine Learning tool suite from Scikit-learn +tool_recommendation_model Create model to recommend tools +virhunter Deep Learning method for novel virus detection in sequencing data +whisper Transcribe audio or video files to text using the OpenAI Whisper. diff --git a/communities/metabolomics/resources/tools.tsv b/communities/metabolomics/resources/tools.tsv deleted file mode 100644 index 2df42996..00000000 --- a/communities/metabolomics/resources/tools.tsv +++ /dev/null @@ -1,183 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 False -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 False -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 False -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 False -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 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qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 False -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 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https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 False -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, 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qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 False -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 False -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 False -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 False -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 False -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 False -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 False -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 False -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 False -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 False +Galaxy wrapper id Description To keep Deprecated +agat GTF/GFF analysis toolkit +ambertools Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. +apoc Large-scale structural comparison of protein pockets +b2btools This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. +bio3d Bio3d is a program that can be used to analyse molecular dynamics trajectories. +biomoldyn Tools for MD analysis +biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. +camera +canonical_correlation_analysis Canonical Correlation Analysis +cardinal Statistical and computational tools for analyzing mass spectrometry imaging datasets +categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. +cell-types-analysis Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis +cemitool Gene co-expression network analysis tool +cfm Competitive Fragmentation Modeling (CFM) +clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy +compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. +compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. +compute_q_values Compute q-values based on multiple simultaneous tests p-values +correlation Correlation for numeric columns +correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis +deseq2 Differential gene expression analysis based on the negative binomial distribution +deseq2_normalization Normalizes gene hitlists +dexseq Inference of differential exon usage in RNA-Seq +dimet DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. +draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria +dropletutils De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 +dwt_cor_ava_perclass Compute P-values and Correlation Coefficients for Feature Occurrences +dwt_cor_avb_all Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features +dwt_ivc_all Compute P-values and Second Moments for Feature Occurrences +dwt_var_perclass Compute P-values and Max Variances for Feature Occurrences +dwt_var_perfeature Wavelet variance using Discrete Wavelet Transfoms +edger Perform RNA-Seq differential expression analysis using edgeR pipeline +egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing +ez_histograms ggplot2 histograms and density plots +fasta_clipping_histogram Length Distribution chart +fastq_quality_boxplot Draw quality score boxplot +fastx_quality_statistics Compute quality statistics +fgsea Perform gene set testing using fgsea +filter_compounds Tool for filtering organometallics/anorganic compounds from a list of compounds. +fisher_test Fisher's exact test on two-column hit lists. +flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. +free_energy Free energy tools of BRIDGE. +garnett De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 +gc_derivatization In silico derivatization for GC. +gcms2isocor Conversion from GCMS PostRun Analysis to Isocor +gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs +genform genform: generation of molecular formulas by high-resolution MS and MS/MS data +genomescope Analyze unassembled short reads +goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data +gprofiler functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more +graphembed Compute a 2D embedding of a data matrix given supervised class information +gromacs GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. +gsc_center_scale Center or scale (standardize) data +heinz An algorithm for identification of the optimal scoring subnetwork. +histogram Histogram of a numeric column +influx_data_manager Handling influx_si data inputs in Galaxy workflows +influx_si metabolic flux estimation based on [in]stationary labeling +intervene Create pairwise and upset plots +ipo [W4M][LC-MS] IPO +isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. +isolib Create an isotopic pattern library for given compounds and adducts. +isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments +iwtomics Interval-Wise Testing for Omics Data +kernel_canonical_correlation_analysis Kernel Canonical Correlation Analysis +kernel_principal_component_analysis Kernel Principal Component Analysis +kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file +lda_analysis Perform Linear Discriminant Analysis +length_and_gc_content Gets gene length and gc content from a fasta and a GTF file +limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline +linear_regression Perform Linear Regression +logistic_regression_vif Perform Logistic Regression with vif +macs2 MACS - Model-based Analysis of ChIP-Seq +mapping_quality_stats Collects and shows the distribution of MAPQ values in a BAM alignment file +masigpro Identify significantly differential expression profiles in time-course microarray experiments +matchms Searching, filtering and converting mass spectral libraries. +mdanalysis MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations +mdfileconverter A tool for interconverting between different MD structure and trajectory file formats. +mdslicer A tool for slicing trajectory files using MDTraj. +mdtraj MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories +metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) +metfrag-vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag +metilene Differential DNA methylation calling +mfassignr The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements +misc +mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model +monocle3 De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. +ms2deepscore Mass spectra similarity scoring using a trained ms2deepscore model. +ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. +msPurity [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data +msmetaenhancer +msp_merge +msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data +multigsea GSEA-based pathway enrichment analysis for multi-omics data +multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report +mzmine mass-spectrometry data processing, with the main focus on LC-MS data +mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. +mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML +nmr_annotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation +nmr_annotation2d [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra +nmr_preprocessing [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction +normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data +numeric_clustering Clustering tool for numberic values +openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." +openmm OpenMM is a toolkit for molecular simulation using high performance GPU code. +packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations +pandas_rolling_window Rolling window calculations +partialr_square Compute partial R square +pathifier pathifier +pathview Pathview is a tool set for pathway based data integration and visualization. +pearson_correlation Pearson and apos Correlation between any two numeric columns +physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes +physiofit_manager Handling of physiofit input files +plot_from_lda "Draw ROC plot on ""Perform LDA"" output" +plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. +poisson2test Poisson two-sample test +principal_component_analysis Principal Component Analysis +probecoverage computes and plots read coverage of genomic regions by sequencing datasets +pyteomics Tools using the pyteomics library +qcxms QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). +ramclustr +rcx-tk Tools to process metadata or alkane files. +rdock Docking ligands to proteins and nucleic acids +recetox_aplcms Peak detection tool for HRMS profile data. +recetox_msfinder +recetox_xmsannotator +rem_complex Removes molecular coordination complexes. +rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results +retip +rgcca multi-block analysis +riassigner +rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. +ruvseq Remove Unwanted Variation from RNA-Seq Data +sc3 De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. +scater De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. +scatterplot Scatterplot of two numeric columns +scmap De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. +scpred De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 +seurat De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 +sklearn Machine Learning tool suite from Scikit-learn +skyline2isocor Converting skyline output to IsoCor input +sleuth Sleuth is a program for differential analysis of RNA-Seq data. +smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization +snpfreq snpFreq significant SNPs in case-control data +spec2vec Mass spectra similarity scoring using a trained Spec2Vec model. +statistics Tool for computing statistical tests. +suite_qiime2__alignment +suite_qiime2__composition +suite_qiime2__cutadapt +suite_qiime2__dada2 +suite_qiime2__deblur +suite_qiime2__demux +suite_qiime2__diversity +suite_qiime2__diversity_lib +suite_qiime2__emperor +suite_qiime2__feature_classifier +suite_qiime2__feature_table +suite_qiime2__fragment_insertion +suite_qiime2__longitudinal +suite_qiime2__metadata +suite_qiime2__phylogeny +suite_qiime2__quality_control +suite_qiime2__quality_filter +suite_qiime2__rescript +suite_qiime2__sample_classifier +suite_qiime2__taxa +suite_qiime2__vsearch +suite_qiime2_core +suite_qiime2_core__tools +t_test_two_samples T Test for Two Samples +tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. +topologyeditors Set of python scripts and associated tool files that can be used to modify topology files. +tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. +vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations +volcanoplot Tool to create a Volcano Plot +w4mclassfilter Filter W4M data by values or metadata +w4mconcatenate [W4M][Utils] concatenate two Metadata tables +w4mcorcov OPLS-DA Contrasts of Univariate Results +w4mjoinpn Join positive- and negative-mode W4M datasets +waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. +xcms +xtb Performs semiempirical molecular optimization. +xy_plot Plotting tool for multiple series and graph types diff --git a/communities/microgalaxy/metadata/tool_status.tsv b/communities/microgalaxy/metadata/tool_status.tsv index ba003585..5c90f2cc 100644 --- a/communities/microgalaxy/metadata/tool_status.tsv +++ b/communities/microgalaxy/metadata/tool_status.tsv @@ -1,3 +1,4 @@ + To keep Deprecated abacas TRUE FALSE abricate TRUE FALSE abritamr TRUE FALSE diff --git a/communities/microgalaxy/resources/tools.tsv b/communities/microgalaxy/resources/curated_tools.tsv similarity index 95% rename from communities/microgalaxy/resources/tools.tsv rename to communities/microgalaxy/resources/curated_tools.tsv index 25913789..97ac00e5 100644 --- a/communities/microgalaxy/resources/tools.tsv +++ b/communities/microgalaxy/resources/curated_tools.tsv @@ -1,291 +1,291 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 True False True -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 True False True -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 True False True -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 True False True -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 True False True -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 True False True -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 True False True -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 True False True -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 True False True -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 True False True -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 True False True -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 True False True -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 True False True -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 True False True -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 True False True -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 True False True -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 True False True -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 True False True -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 True False True -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 True False True -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 True False True -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 True False True -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 True False True -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 True False True -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 True False True -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 True False True -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 True False True -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 True False True -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 True False True -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 True False True -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 True False True -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 True False True -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 True False True -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 True False True -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 True False True -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 True False True -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 True False True -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 True False True -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 True False True -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 True False True -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 True False True -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 True False True -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 True False True -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 True False True -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 True False True -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 True False True -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 True False True -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 True False True -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 True False True -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 True False True -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 True False True -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 True False True -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 True False True -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 True False True -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 True False True -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 True False True -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 True False True -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 True False True -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 True False True -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True False True -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 True False True -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 True False True -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 True False True -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 True False True -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 True False True -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 True False True -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 True False True -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 True False True -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 True False True -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 True False True -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 True False True -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 True False True -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 True False True -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 True False True -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 True False True -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 True False True -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 True False True -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 True False True -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 True False True -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 True False True -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 True False True -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 True False True -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 True False True -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 True False True -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 True False True -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 True False True -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 True False True -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 True False True -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 True False True -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 True False True -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 True False True -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 True False True -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 True False True -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 True False True -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 True False True -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 True False True -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 True False True -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 True False True -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 True False True -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 True False True -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 True False True -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 True False True -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 True False True -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 True False True -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 True False True -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 True False True -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 True False True -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True False True -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 True False True -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 True False True -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 True False True -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 True False True -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 True False True -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 True False True -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 True False True -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 True False True -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 True False True -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 True False True -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 True False True -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 True False True -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 True False True -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 True False True -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 True False True -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 True False True -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 True False True -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 True False True -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 True False True -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 True False True -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 True False True -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 True False True -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 True False True -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 True False True -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 True False True -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 True False True -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 True False True -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 True False True -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 True False True -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 True False True -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 True False True -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 True False True -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 True False True -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 True False True -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 True False True -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 True False True -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 True False True -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 True False True -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 True False True -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 True False True -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 True False True -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 True False True -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 True False True -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 True False True -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 True False True -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 True False True -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 True False True -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 True False True -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 True False True -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 True False True -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 True False True -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 True False True -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 True False True -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 True False True +Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed To keep Deprecated +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 True True False +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 True True False +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 True True False +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 True True False +abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 True True False +aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 True True False +amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 True True False +amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 True True False +ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 True True False +antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 True True False +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 True True False +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 True True False +bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 True True False +bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 True True False +bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 True True False +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 True True False +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 True True False +binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 True True False +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 True True False +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 True True False +blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 True True False +blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 True True False +blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 True True False +bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 True True False +busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 True True False +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 True True False +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 True True False +cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 True True False +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True True False +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 True True False +clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 True True False +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 True True False +clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 True True False +cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 True True False +codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 True True False +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 True True False +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 True True False +compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 True True False +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 True True False +concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 True True False +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 True True False +cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 True True False +cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 True True False +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 True True False +das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 True True False +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True True False +diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 True True False +disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 True True False +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 True True False +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 True True False +ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 True True False +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 True True False +emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 True True False +ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 True True False +export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 True True False +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 True True False +fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 True True False +fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 True True False +fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 True True False +fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 True True False +fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 True True False +featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True True False +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 True True False +flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 True True False +flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 True True False +format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 True True False +fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 True True False +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 True True False +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 True True False +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 True True False +gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 True True False +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 True True False +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 True True False +goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 True True False +graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 True True False +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 True True False +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 True True False +gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 True True False +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 True True False +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 True True False +hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 True True False +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 True True False +humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 True True False +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 True True False +hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 True True False +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 True True False +infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 True True False +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 True True False +integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 True True False +interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 True True False +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 True True False +isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 True True False +itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 True True False +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 True True False +jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 True True False +jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 True True False +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 True True False +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 True True False +kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 True True False +kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 True True False +kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 True True False +kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 True True False +kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 True True False +kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 True True False +kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 True True False +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 True True False +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 True True False +legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 True True False +lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 True True False +limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True True False +lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 True True False +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 True True False +lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 True True False +m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 True True False +maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 True True False +mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 True True False +make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 True True False +mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 True True False +mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 True True False +maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 True True False +maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 True True False +mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 True True False +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 True True False +megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 True True False +megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 True True False +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 True True False +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 True True False +meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 True True False +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 True True False +metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 True True False +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 True True False +metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 True True False +metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 True True False +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 True True False +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 True True False +minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 True True False +miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 True True False +minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 True True False +miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 True True False +mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 True True False +mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 True True False +mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 True True False +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 True True False +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 True True False +msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 True True False +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True True False +multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 True True False +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 True True False +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 True True False +nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 True True False +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 True True False +ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 True True False +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 True True False +newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 True True False +nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 True True False +nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 True True False +nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 True True False +nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 True True False +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 True True False +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 True True False +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 True True False +orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 True True False +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 True True False +peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 True True False +pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 True True False pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 True False True -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 True False True -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 True False True -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 True False True -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 True False True -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 True False True -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 True False True -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 True False True -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 True False True -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 True False True -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 True False True -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 True False True -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 True False True -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 True False True -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 True False True -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True False True -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 True False True -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 True False True -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 True False True -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 True False True -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 True False True -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 True False True -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 True False True -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 True False True -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True False True -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 True False True -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 True False True -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 True False True -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 True False True -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 True False True -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 True False True -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 True False True -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 True False True -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 True False True -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 True False True -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 True False True -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 True False True -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 True False True -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 True False True -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 True False True -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 True False True -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 True False True -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True False True -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True False True -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 True False True -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 True False True -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 True False True -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 True False True -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 True False True -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 True False True -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 True False True -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 True False True -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 True False True -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 True False True -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 True False True -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 True False True -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 True False True -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 True False True -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 True False True -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 True False True -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 True False True -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 True False True -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 True False True -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 True False True -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 True False True -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 True False True -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 True False True -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 True False True -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 True False True -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 True False True -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 True False True -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 True False True -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 True False True -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 True False True -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 True False True -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 True False True -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 True False True -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 True False True -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 True False True -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 True False True -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 True False True -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 True False True -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 True False True -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 True False True -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 True False True -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 True False True -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 True False True -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 True False True -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 True False True -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 True False True + " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 True True False +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 True True False +phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 True True False +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 True True False +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 True True False +plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 True True False +plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 True True False +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 True True False +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 True True False +prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 True True False +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 True True False +pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 True True False +pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 True True False +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 True True False +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 True True False +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True True False +quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 True True False +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 True True False +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 True True False +raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 True True False +read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 True True False +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 True True False +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 True True False +roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 True True False +rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True True False +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True True False +sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 True True False +sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 True True False +scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 True True False +semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 True True False +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 True True False +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 True True False +seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 True True False +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 True True False +sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 True True False +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 True True False +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 True True False +snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 True True False +sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 True True False +sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 True True False +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 True True False +spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 True True False +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 True True False +srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True True False +srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True True False +staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 True True False +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 True True False +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 True True False +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 True True False +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 True True False +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 True True False +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 True True False +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 True True False +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 True True False +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 True True False +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 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https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 True True False +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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+suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 True True False +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 True True False +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 True True False +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 True True False +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 True True False +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 True True False +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 True True False +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 True True False +t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 True True False +t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 True True False +t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 True True False +taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 True True False +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 True True False +tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 True True False +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 True True False +transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 True True False +trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 True True False +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 True True False +unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 True True False +unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 True True False +uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 True True False +usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 True True False +valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 True True False +vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 True True False +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 True True False +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 True True False +velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 True True False +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 True True False +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 True True False +vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 True True False +wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 True True False diff --git a/communities/microgalaxy/resources/curated_tools_w_biotools.tsv b/communities/microgalaxy/resources/curated_tools_w_biotools.tsv new file mode 100644 index 00000000..fbc3e0ef --- /dev/null +++ b/communities/microgalaxy/resources/curated_tools_w_biotools.tsv @@ -0,0 +1,219 @@ +Galaxy wrapper id bio.tool name EDAM operation EDAM topic +TreeBest TreeBeST Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics +abricate ABRicate Antimicrobial resistance prediction Genomics, Microbiology +abritamr abriTAMR Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease +abyss ABySS Genome assembly, De-novo assembly, Scaffolding Sequence assembly +aldex2 ALDEx2 Statistical inference Gene expression, Statistics and probability +amplican amplican Alignment, Standardisation and normalisation PCR experiment, Statistics and probability +amrfinderplus AMRFinderPlus Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease +ancombc ANCOMBC DNA barcoding Microbial ecology, Metagenomics, Taxonomy +antismash antiSMASH Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families +artic ARTIC Sequence alignment Genomics +bakta Bakta Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis +bamtools BamTools Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis +bandage Bandage Sequence assembly visualisation Genomics, Sequence assembly +bayescan BayeScan Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism +bbtools BBMap RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq +bigscape BiG-SCAPE Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families +binning_refiner Binning_refiner Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology +biom_format biomformat Formatting Laboratory information management, Sequence analysis +biotradis biotradis Sequence analysis Mobile genetic elements, Workflows +bracken Bracken Statistical calculation Metagenomics, Microbial ecology +busco BUSCO Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis +cat CAT and BAT Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly +cdhit cd-hit Sequence clustering Sequencing +cemitool CEMiTool Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment +checkm CheckM Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management +clair3 Clair3 Variant calling Molecular genetics +clinod clinod Nucleic acid sequence analysis Sequence analysis +clustalw Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment Phylogeny, Sequence analysis +cmsearch_deoverlap cmsearch-deoverlap Comparison, Alignment Biology, Medicine +codeml PAML Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis +cojac COJAC Genetic variation +combine_metaphlan_humann Combine Metaphlan and HUMAnN Aggregation Metagenomics, Molecular interactions, pathways and networks +compare_humann2_output Compare HUMAnN2 outputs Comparison Metagenomics, Gene and protein families +compleasm compleasm Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis +concoct CONCOCT Sequence clustering, Read binning Metagenomics +coverm CoverM Local alignment Bioinformatics +cutadapt Cutadapt Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing +dada2 dada2 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics +das_tool dastool Read binning Metagenomics +deseq2 DESeq2 Differential gene expression analysis, RNA-Seq analysis RNA-Seq +diamond Diamond Sequence alignment analysis Sequence analysis, Proteins +disco DISCO Protein sequence analysis Structure determination +dram DRAM Gene functional annotation Metagenomics, Biological databases, Molecular genetics +drep dRep Genome comparison Metagenomics, Genomics, Sequence analysis +effectiveT3 EffectiveT3 Sequence classification Sequence analysis +eggnog_mapper eggNOG-mapper v2 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis +emboss_5 EMBOSS Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology +ete ete Phylogenetic analysis, Phylogenetic tree editing Phylogenetics +export2graphlan export2graphlan Conversion Taxonomy, Metabolomics, Biomarkers +fargene fARGene Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology +fastani FastANI Genome alignment, Sequence similarity search Microbiology, Genetic variation +fastp fastp Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers +fastqe FASTQE Sequencing quality control Sequence analysis, Sequencing +fasttree FastTree Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis +featurecounts FeatureCounts Read summarisation, RNA-Seq quantification RNA-Seq +filtlong Filtlong Filtering, Sequencing quality control +flashlfq FlashLFQ Label-free quantification Proteomics experiment, Proteomics +flye Flye Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics +format_metaphlan2_output Format metaphlan2 output Formatting Taxonomy, Metagenomics +fraggenescan FragGeneScan Gene prediction Genetics, Sequence analysis +freyja Freyja RNA-Seq quantification Metagenomics +frogs FROGS Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing +funannotate funannotate Genome annotation Genomics +ggplot2 ggplot2 Visualisation Data visualisation +gi2taxonomy gi2taxonomy Database search, ID mapping Taxonomy +glimmer GEMINI Sequence analysis, Genetic variation analysis Sequence analysis +goenrichment GOEnrichment Gene-set enrichment analysis Transcriptomics +goseq GOseq Gene functional annotation RNA-Seq +graphlan GraPhlAn Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics +graphmap graphmap Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing +gtdbtk GTDB-Tk Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins +gubbins Gubbins Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing +hamronization hAMRonization Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics +hansel BioHansel Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science +hifiasm_meta Hifiasm-meta Sequence assembly Sequence assembly, Metagenomics +hmmer3 HMMER3 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families +humann humann Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics +hyphy HyPhy Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks +hypo HyPo Optimisation and refinement, Genome assembly Sequence assembly, Genomics +icescreen ICEscreen Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation +idba_ud IDBA Sequence assembly Sequence assembly +infernal Infernal Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics +instrain InStrain SNP detection, Genome comparison Mapping, Metagenomics +integron_finder Integron Finder Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis +interproscan InterProScan (EBI) Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis +iqtree iqtree Phylogenetic analysis, Sequence analysis Phylogenetics +isescan ISEScan Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation +itsx ITSx Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology +jbrowse JBrowse Genome visualisation Genomics +jellyfish Jellyfish k-mer counting Sequence analysis, Genomics +kc-align kc-align Multiple sequence alignment Mapping +khmer khmer Standardisation and normalisation, De-novo assembly Sequence assembly +kleborate Kleborate Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing +kofamscan kofamscan Sequence analysis, Gene functional annotation Genomics +kraken Kraken Taxonomic classification Taxonomy, Metagenomics +kraken2 kraken2 Taxonomic classification Taxonomy, Metagenomics +kraken_taxonomy_report Kraken-Taxonomy-Report Visualisation, Classification Metagenomics, Taxonomy +krakentools KrakenTools Visualisation, Aggregation Taxonomy, Metagenomics +krocus krocus Multilocus sequence typing, k-mer counting Public health and epidemiology +legsta legsta Sequence analysis Public health and epidemiology +lighter Lighter k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics +limma_voom limma RNA-Seq analysis Molecular biology, Genetics +lineagespot lineagespot Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation +lorikeet lorikeet Sequence analysis, Genotyping Genotype and phenotype +lotus2 lotus2 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology +m6anet m6Anet Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning +maaslin2 MaAsLin2 Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability +mafft MAFFT Multiple sequence alignment Sequence analysis +maker MAKER Genome annotation Genomics, DNA, Sequence analysis +mapseq MAPseq k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs +mash Mash Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation +maxbin2 MaxBin Sequence assembly Metagenomics, Sequence assembly, Microbiology +maxquant MaxQuant Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability +mcl MCL Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks +medaka Medaka Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning +megahit MEGAHIT Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly +megahit_contig2fastg MEGAHIT Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly +megan MEGAN Sequence analysis, Taxonomic classification Sequence analysis +meningotype meningotype Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype +merqury Merqury Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology +meryl Meryl k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing +metabat2 MetaBAT 2 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing +metaeuk MetaEuk Homology-based gene prediction Metagenomics, Gene and protein families +metagene_annotator MetaGeneAnnotator Sequence annotation Genomics, Model organisms, Data submission, annotation and curation +metagenomeseq metagenomeSeq Sequence visualisation, Statistical calculation Metagenomics, Sequencing +metanovo MetaNovo Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules +metaphlan MetaPhlAn Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics +metaquantome metaQuantome Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics +metawrapmg MetaWRAP Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics +minia Minia Genome assembly Sequence assembly +miniasm miniasm De-novo assembly Genomics, Sequence assembly +minipolish minipolish Localised reassembly, Read depth analysis Sequence assembly, Sequencing +miniprot miniprot Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis +mitos MITOS Genome annotation Zoology, Whole genome sequencing +mlst MLST Multilocus sequence typing Immunoproteins and antigens +mothur mothur DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny +msconvert msConvert Filtering, Formatting Proteomics, Proteomics experiment +multigsea multiGSEA Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules +multiqc MultiQC Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics +mykrobe Mykrobe Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics +mz_to_sqlite mzToSQLite Conversion, Peptide database search Proteomics, Biological databases +nanocompore Nanocompore Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites +nanoplot NanoPlot Scatter plot plotting, Box-Whisker plot plotting Genomics +nanopolishcomp NanopolishComp Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation +ncbi_fcs_gx NCBI fcs Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly +newick_utils Newick Utilities Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science +nextclade Nextclade Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics +nextdenovo NextDenovo De-novo assembly, Genome assembly Sequencing, Sequence assembly +nonpareil nonpareil Operation +nucleosome_prediction nucleosome_prediction Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs +nugen_nudup NuDup Duplication detection Sequencing +obitools OBITools Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing +omark OMArk Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability +orfipy orfipy Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules +orthofinder OrthoFinder Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis +pfamscan PfamScan Protein sequence analysis Sequence analysis +pharokka Pharokka Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA +phyloseq phyloseq Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics +phyml PhyML Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics +picrust PICRUSt Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing +picrust2 PICRUSt2 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing +plasflow PlasFlow Sequence analysis Metagenomics +plasmidfinder PlasmidFinder Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers +polypolish Polypolish Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping +prodigal Prodigal Genome annotation Genomics, Sequence analysis +prokka Prokka Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology +proteinortho Proteinortho Sequence clustering, Sequence analysis Comparative genomics +pycoqc pycoQC Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing +pygenometracks pyGenomeTracks Visualisation, Formatting Model organisms, Imaging, Workflows +qiime_add_on qiime_add_on Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics +qiime_core qiime_core Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics +qualimap QualiMap Sequencing quality control Data quality management +quast QUAST Visualisation, Sequence assembly validation Sequence assembly +quickmerge quickmerge Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype +racon Racon Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly +rasusa rasusa +raxml RAxML Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis +read_it_and_keep read_it_and_keep Filtering, Genome alignment Pathology, Genomics +reago REAGO Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology +recentrifuge Recentrifuge Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing +roary Roary Genome assembly DNA, Genomics, Mapping +rseqc RSeQC Data handling Sequencing +salmon Salmon Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics +scoary Scoary Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics +semibin SemiBin Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly +seqkit seqkit DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis +seqprep SeqPrep Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers +seqsero2 SeqSero2 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics +shorah ShoRAH Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics +shovill shovill Genome assembly Genomics, Microbiology, Sequence assembly +smallgenomeutilities V-pipe Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing +snap SNAP Gene prediction DNA, DNA polymorphism, Genetics +snippy snippy Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics +sonneityping sonneityping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics +sortmerna SortMeRNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics +spades SPAdes Genome assembly Sequence assembly +spotyping SpoTyping Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation +srst2 srst2 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology +structure Structure Genetic variation analysis Population genetics +t2ps Draw phylogeny Phylogenetic tree visualisation Phylogenomics +taxonomy_krona_chart Krona Visualisation Metagenomics +tb-profiler tb-profiler Antimicrobial resistance prediction +tooldistillator ToolDistillator Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis +transit TRANSIT Transposon prediction DNA, Sequencing, Mobile genetic elements +transtermhp TransTermHP Transcriptional regulatory element prediction Transcription factors and regulatory sites +trim_galore Trim Galore Sequence trimming, Primer removal, Read pre-processing Sequence analysis +unicycler Unicycler Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly +unipept Unipept Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows +usher usher Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics +valet VALET Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly +vapor VAPOR Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly +varvamp varVAMP PCR primer design Virology, Probes and primers +vegan vegan Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science +velvet Velvet Formatting, De-novo assembly Sequence assembly +velvet_optimiser VelvetOptimiser Optimisation and refinement, Sequence assembly Genomics, Sequence assembly +virAnnot virAnnot Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology +vsearch VSEARCH DNA mapping, Chimera detection Metagenomics, Sequence analysis +wtdbg wtdbg2 Genome assembly, De-novo assembly Sequence assembly, Sequencing diff --git a/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv b/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv new file mode 100644 index 00000000..931456ba --- /dev/null +++ b/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv @@ -0,0 +1,71 @@ +Galaxy wrapper id Source Galaxy wrapper source +PAMPA https://github.com/ColineRoyaux/PAMPA-Galaxy +abacas https://github.com/phac-nml/abacas https://github.com/phac-nml/abacas +assemblystats https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools +biohansel https://github.com/phac-nml/biohansel https://github.com/phac-nml/biohansel +blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go +blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh +blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr +cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup +combine_assembly_stats https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools +cryptogenotyper https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/CryptoGenotyper +ectyper https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/ecoli_serotyping +ez_histograms https://github.com/tidyverse/ggplot2 https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms +fastk https://github.com/thegenemyers/FASTK https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk +filter_spades_repeats https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/ +getmlst +glimmer_hmm https://ccb.jhu.edu/software/glimmerhmm/ https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm +hivtrace https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace +iprscan5 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 +ivar https://github.com/andersen-lab/ivar https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ +kat_filter +kraken2tax https://bitbucket.org/natefoo/taxonomy https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ +kraken_biom https://github.com/smdabdoub/kraken-biom https://github.com/smdabdoub/kraken-biom +lca_wrapper https://bitbucket.org/natefoo/taxonomy https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper +make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr +mob_suite https://github.com/phac-nml/mob-suite https://github.com/phac-nml/mob-suite +mrbayes +msstatstmt http://msstats.org/msstatstmt/ https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt +mykrobe_parser https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/mykrobe-parser +ncbi_blast_plus https://blast.ncbi.nlm.nih.gov/ https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus +obisindicators https://github.com/Marie59/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators +peptideshaker http://compomics.github.io https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker +plasmidspades +promer https://github.com/phac-nml/promer https://github.com/phac-nml/promer +rRNA http://weizhong-lab.ucsd.edu/meta_rna/ https://github.com/bgruening/galaxytools/tree/master/tools/rRNA +repeatexplorer2 https://github.com/repeatexplorer/repex_tarean https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 +sarscov2formatter https://github.com/nickeener/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter +sarscov2summary https://github.com/nickeener/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary +sistr_cmd https://github.com/phac-nml/sistr_cmd +smalt http://www.sanger.ac.uk/science/tools/smalt-0 https://sourceforge.net/projects/smalt/ +sr_bowtie http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie +srst2 +staramr https://github.com/phac-nml/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr +stringmlst +suite_qiime2__alignment https://github.com/qiime2/q2-alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment +suite_qiime2__composition https://github.com/qiime2/q2-composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition +suite_qiime2__cutadapt https://github.com/qiime2/q2-cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt +suite_qiime2__dada2 http://benjjneb.github.io/dada2/ https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 +suite_qiime2__deblur https://github.com/biocore/deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur +suite_qiime2__demux https://github.com/qiime2/q2-demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux +suite_qiime2__diversity https://github.com/qiime2/q2-diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity +suite_qiime2__diversity_lib https://github.com/qiime2/q2-diversity-lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib +suite_qiime2__emperor http://emperor.microbio.me https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor +suite_qiime2__feature_classifier https://github.com/qiime2/q2-feature-classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier +suite_qiime2__feature_table https://github.com/qiime2/q2-feature-table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table +suite_qiime2__fragment_insertion https://github.com/qiime2/q2-fragment-insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion +suite_qiime2__longitudinal https://github.com/qiime2/q2-longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal +suite_qiime2__metadata https://github.com/qiime2/q2-metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata +suite_qiime2__phylogeny https://github.com/qiime2/q2-phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny +suite_qiime2__quality_control https://github.com/qiime2/q2-quality-control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control +suite_qiime2__quality_filter https://github.com/qiime2/q2-quality-filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter +suite_qiime2__rescript https://github.com/nbokulich/RESCRIPt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript +suite_qiime2__sample_classifier https://github.com/qiime2/q2-sample-classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier +suite_qiime2__taxa https://github.com/qiime2/q2-taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa +suite_qiime2__vsearch https://github.com/qiime2/q2-vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch +suite_qiime2_core +suite_qiime2_core__tools https://qiime2.org https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools +t2t_report https://bitbucket.org/natefoo/taxonomy https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report +t_coffee http://www.tcoffee.org/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee +trycycler https://github.com/rrwick/Trycycler https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler +uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader diff --git a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json new file mode 100644 index 00000000..9760a20c --- /dev/null +++ b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json @@ -0,0 +1,76549 @@ +[ + { + "Galaxy wrapper id": "braker", + "Galaxy tool ids": [ + "braker" + ], 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Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)", + "EDAM operation": [ + "Genome indexing", + "Antimicrobial resistance prediction", + "Genome alignment" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Sequence assembly", + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/denglab/SeqSero2", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqsero2", + "Date of first commit of the suite": "2023-11-07", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", + "Galaxy wrapper version": "1.3.1", + "Conda id": "seqsero2", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [ + "Genome indexing", + "Antimicrobial resistance prediction", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Sequence assembly", + "Genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 0, + "Tools available on CropGalaxy": 0, + "Tools available on Dintor": 0, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 0, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 0, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 0, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 0, + "Tools available on PhagePromotor": 0, + "Tools available on UseGalaxy.be": 0, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0, + "Tools available on Viral Variant Visualizer (VVV)": 0, + "No. of tool users (5 years) (usegalaxy.eu)": 4182, + "No. of tool users (all time) (usegalaxy.eu)": 4182, + "Tool usage (5 years) (usegalaxy.eu)": 42, + "Tool usage (all time) (usegalaxy.eu)": 42, + "No. of tool users (5 years) (usegalaxy.org)": 0, + "No. of tool users (all time) (usegalaxy.org)": 0, + "Tool usage (5 years) (usegalaxy.org)": 0, + "Tool usage (all time) (usegalaxy.org)": 0, + "No. of tool users (5 years) (usegalaxy.org.au)": 0, + "No. of tool users (all time) (usegalaxy.org.au)": 0, + "Tool usage (5 years) (usegalaxy.org.au)": 0, + "Tool usage (all time) (usegalaxy.org.au)": 0, + "No. of tool users (5 years) - all main servers": 4182, + "No. of tool users (all time) - all main servers": 4182, + "Tool usage (5 years) - all main servers": 42, + "Tool usage (all time) - all main servers": 42, + "Reviewed": true, + "To keep": true, + "Deprecated": false + }, + { + "Galaxy wrapper id": "seqtk", + "Galaxy tool ids": [ + "seqtk_comp", + "seqtk_cutN", + "seqtk_dropse", + "seqtk_fqchk", + "seqtk_hety", + "seqtk_listhet", + "seqtk_mergefa", + "seqtk_mergepe", + "seqtk_mutfa", + "seqtk_randbase", + "seqtk_sample", + "seqtk_seq", + "seqtk_subseq", + "seqtk_telo", + "seqtk_trimfq" + ], + "Description": "Toolkit for processing sequences in FASTA/Q formats", + "bio.tool id": "seqtk", + "bio.tool ids": [ + "seqtk" + ], + "biii": null, + "bio.tool name": "seqtk", + "bio.tool description": "A tool for processing sequences in the FASTA or FASTQ format. 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 True False False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 True False False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 True False False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 True False False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 True False False -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 True False False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 True False False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 True False False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 True False False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 True False False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 True False False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 True False False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 True False True -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 True False False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 True False False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 True False False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 True False False -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 True False False -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 True False True -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 True False False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 True False True -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 True False True -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 True False True -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 True False False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 True False False -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 True False True -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 True False False -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 True False True -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 True False False -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 True False True -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 True False True -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 True False False -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 True False False -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 True False True -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 True False False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 True False False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 True False False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 True False True -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 False -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 True False False -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 True False False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 True False False -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 True False True -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 True False False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 True False True -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 True False False -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 True False False -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 True False False -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 True False True -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False False -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 True False False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 True False False -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 True False True -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 True False True -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 True False False -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 True False False -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 True False False -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 True False False -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 True False True -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 False -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 True False True -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 True False False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 True False True -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 True False False -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 True False False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 True False True -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 True False False -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 True False False -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 True False True -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 True False False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 True False True -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 True False False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 True False False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 True False False -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 True False True -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 True False False -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 True False False -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 True False False -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 True False True -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 True False False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 True False False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 True False False -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 True False False -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 True False True -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 True False False -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 True False False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 True False False -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 True False False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 True False False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 True False True -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 True False True -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 True False True -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 True False False -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 True False False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 True False True -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 True False False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 True False False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 True False False -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 True False False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 True False False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 True False False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 True False True -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 True False False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 True False True -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 True False True -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 True False True -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 True False False -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 True False True -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 True False False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 True False True -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 True False False -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 True False False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 True False False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 True False True -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 True False False -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 True False True -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 True False True -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 True False False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 True False False -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 True False True -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 True False False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 True False False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 True False True -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 True False False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False False -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 True False False -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 True False True -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 True False False -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 True False False -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 True False False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 True False True -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 True False True -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 True False True -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 True False False -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 True False False -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 True False False -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 True False False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 True False False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False False -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 True False False -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 True False False -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 True False True -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 True False False -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 True False False -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 True False False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 True False True -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 True False False -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 True False False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 True False False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 True False True -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 True False True -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 True False False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 True False True -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 True False True -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 True False True -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 True False False -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 True False True -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 True False False -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 True False False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 True False True -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 True False False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 False -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 True False True -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 True False False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 True False False -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 True False False -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 True False True -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 True False False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 True False True -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 True False True -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 True False True -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 True False True -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 True False False -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 True False False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True False True -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 True False False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 True False False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 True False False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 True False True -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 True False False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 True False False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 True False False -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 True False True -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 True False True -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 True False True -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 True False True -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 False -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 True False True -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 True False True -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False False -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 True False False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 True False False -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 True False False -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 True False False -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 True False False -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 True False False -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 True False False -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 True False False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 True False False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 True False False -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 True False False -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 True False False -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 True False False -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 True False False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 True False True -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 True False True -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 True False True -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 True False False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 True False True -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 True False True -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 True False False -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 True False False -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 True False True -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 True False True -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 True False False -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 True False True -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 True False False -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 True False True -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 True False False -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 True False True -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 True False True -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 True False False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 True False False -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 True False False -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 True False False -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 True False False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 True False False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 True False False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 True False False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 True False False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 True False False -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 True False False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 True False True -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 True False False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 True False False -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 True False True -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 True False False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 True False False -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 True False False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 True False True -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 True False False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 True False True -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 True False True -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 True False True -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 True False False -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 True False False -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 True False False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 True False False -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 True False True -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 True False False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 True False True -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 True False False -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 True False True -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 True False False -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 True False True -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 True False True -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 True False True -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 True False False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 True False False -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 True False True -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 True False True -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 True False True -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 False -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 True False False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 True False True -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 True False True -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 True False True -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 True False True -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 True False True -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 True False True -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 True False True -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 True False True -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 True False True -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 True False True -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 True False True -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 True False False -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 True False True -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 True False True -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 True False False -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 True False False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 True False True -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True False True -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 True False True -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 True False False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 True False False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 True False False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 True False True -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 True False True -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 True False True -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 True False True -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 True False False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 True False False -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 True False True -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 True False True -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 True False False -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 True False False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 True False True -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 True False True -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 True False False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 True False False -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 True False True -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 True False True -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 True False True -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 True False False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 True False False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 True False True -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 True False False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 True False True -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 True False True -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 True False True -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 True False True -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 True False False -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 True False True -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 True False True -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 True False True -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 True False True -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 True False True -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 True False True -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 True False True -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 True False True -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 True False False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 True False False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 True False False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 True False False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 True False False -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 True False False -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 True False False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 True False True -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 True False True -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 True False True -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 True False True -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 True False False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 True False False -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 True False False -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 True False False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 True False False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 True False False -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 True False True -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 True False True -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 True False False -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 True False True -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False False -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 True False False -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 True False True -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 True False False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 True False False -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 True False True -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 True False False -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 True False False -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 True False False -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 True False True -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 True False False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 True False True -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 True False False -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 True False False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 True False True -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 True False False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 True False True -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 True False True -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 True False True -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 True False False -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 True False True -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 True False False -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 True False True -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 True False False -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 True False True -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 True False True -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 True False True -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 True False True -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 True False False -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 True False True -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 True False True -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 True False True -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 True False False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 True False False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 True False False -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 True False True -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 True False False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 True False False -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 True False False -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 True False False -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 True False True -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 True False True -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 True False False -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 True False False -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 True False False -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 True False False -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 True False False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 True False False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 True False False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 True False False -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 True False False -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 True False False -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 True False False -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 True False False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 True False True -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 True False False -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 True False True -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 True False True -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 True False True -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 True False True -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 True False True -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 True False True -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 True False False -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 True False False -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 True False True -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 True False True -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 True False False -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 True False False -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 True False False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 True False False -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 True False True -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 True False False -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 True False False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 True False False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 True False True -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 True False False -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 True False True -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 True False False -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 True False False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 True False False -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 True False False -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 True False True -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 True False False -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 True False False -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 True False False -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 True False False -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 True False False -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 True False False -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 True False False -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 True False False -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 True False False -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 True False False -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 True False False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 True False False -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 True False False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 True False False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 True False True -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 True False True -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 True False False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 True False False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 True False False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 True False True -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 True False True -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 False -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True False True -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 True False False -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 True False False -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 True False False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 True False False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 True False True -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 True False True -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 True False False -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 True False False -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 True False True -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 True False False -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 True False False -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 True False True -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 True False False -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 True False False -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 True False False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 True False True -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 True False True -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 True False False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 True False False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 True False False -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 True False False -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 True False False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 True False True -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 True False False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 True False False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 True False False -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 True False False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 True False False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 True False False -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 True False False -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 True False False -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 True False False -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 True False False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 True False False -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 True False False -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 True False False -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 True False True -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 True False False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True False True -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 True False False -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 True False False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 True False False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 True False False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 True False False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 True False False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 True False False -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 True False True -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 True False True -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 True False False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False False -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 True False True -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 True False False -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 True False False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 True False True -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 True False False -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 True False False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 True False False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 True False False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 True False False -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 True False False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 True False True -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 True False True -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 True False True -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 True False False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 True False False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 True False False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 True False False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 True False True -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 True False False -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 True False False -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 True False True -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 True False False -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 True False False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 True False False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 True False True -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 True False False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 True False True -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 True False False -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 True False False -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 True False True -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 True False False -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 True False True -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 True False True -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 True False True -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 True False False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 True False False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 True False True -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 True False True -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 True False False -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True False True -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 True False True -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 True False False -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 True False False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 True False False -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 True False False -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 True False True -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 True False False -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 True False True -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 True False False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 True False False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 True False True -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 True False True -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 True False True -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 True False True -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 True False True -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 True False True -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 True False True 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-suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 True False True -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 True False True -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 True False True 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 True False True -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 True False True -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 True False True -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 True False True -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 True False True -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 True False True -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 True False True -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 True False True -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 True False False -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 True False True -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 True False True -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 True False True -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 True False False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 True False False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 True False False -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 True False True -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 False -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 True False True -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 True False False -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 True False False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 True False False -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 True False False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 True False False -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 False -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 True False False -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 True False True -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 True False False -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 True False False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 True False False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 True False True -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 True False False -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 True False False -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 True False True -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 True False True -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 True False False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 True False False -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 True False False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 True False True -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 True False False -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 True False False -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 True False True -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 True False True -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 True False False -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 True False True -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 True False True -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 True False True -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 True False False -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 True False True -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 True False True -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 True False True -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 True False True -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 True False True -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 True False False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 True False False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 True False False -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 True False False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 True False False -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 True False True -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 True False True -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 True False False -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 True False False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 True False False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 True False True -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 True False False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 True False False -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 True False False +Galaxy wrapper id Description To keep Deprecated +AggregateAlignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. False False +AlignCluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. False False +CMFinder Determines consensus motives for sequences. False False +CollectResults Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. False False +CollectResultsNoAlign Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. False False +EMLassemblyline Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa False False +Ecoregionalization_workflow Tools to compute ecoregionalization with BRT model predictions and clustering. False False +GAFA Gene Align and Family Aggregator False False +GSPAN Second step of GraphClust False False +Geom_mean_workflow Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). False False +LocARNAGraphClust MLocARNA computes a multiple sequence-structure alignment of RNA sequences. False False +NSPDK Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. False False +PAMPA Tools to compute and analyse biodiversity metrics True False +Plotting Plotting results for GraphClust False False +PrepareForMlocarna This tool prepares files for locarna step. False False +Preprocessing Preprocessing input for GraphClust False False +Structure_GSPAN Convert RNA structure to GSPAN graphs False False +ThermoRawFileParser Thermo RAW file converter False False +TreeBest TreeBeST best True False +TrimNs TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline False False +abacas Order and Orientate Contigs True False +abricate Mass screening of contigs for antiobiotic resistance genes True False +abritamr A pipeline for running AMRfinderPlus and collating results into functional classes True False +abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler True False +adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. False False +aegean AEGeAn toolkit wrappers False False +aldex2 Performs analysis Of differential abundance taking sample variation into account True False +align_back_trans Thread nucleotides onto a protein alignment (back-translation) False False +amplican AmpliCan is an analysis tool for genome editing. True False +ampvis2 ampvis2 False False +amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." True False +ancombc Performs analysis of compositions of microbiomes with bias correction. True False +annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages False False +antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . False False +antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters True False +aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. +aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. +aresite2 AREsite2 REST Interface False False +argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database +arriba Arriba detects fusion genes in RNA-Seq data after running RNA-STAR False False +art Simulator for Illumina, 454, and SOLiD sequencing data False False +artic The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building True False +assembly-stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. False False +assemblystats Summarise an assembly (e.g. N50 metrics) True False +astral Tool for estimating an unrooted species tree given a set of unrooted gene trees +augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. False False +augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. False False +b2btools This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. False False +bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" True False +bam2mappingstats Generates mapping stats from a bam file. False False +bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. False False +bamhash Hash BAM and FASTQ files to verify data integrity False False +bamparse Generates hit count lists from bam alignments. False False +bamtools Operate on and transform BAM datasets in various ways using bamtools True False +bamtools_filter Filter BAM datasets on various attributes using bamtools filter False False +bamtools_split Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. False False +bamutil bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. False False +bandage Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily True False +barcode_collapse Paired End randomer aware duplicate removal algorithm False False +baredsc baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. False False +barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. False False +baseline_calculator Toxicity prediction using QSAR models +bax2bam BAX to BAM converter False False +bayescan Detecting natural selection from population-based genetic data True False +bbtools BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. True False +bctools bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 False False +bed_to_protein_map Converts a BED file to a tabular list of exon locations False False +bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. False False +best_regression_subsets Perform Best-subsets Regression False False +bigscape Construct sequence similarity networks of BGCs and groups them into GCF True False +bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files +binning_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. True False +biohansel Heidelberg and Enteritidis SNP Elucidation True False +bioinformatics_cafe Miscellanea of scripts for bioinformatics False False +biom_format The biom-format package provides a command line interface and Python API for working with BIOM files. True False +bionano Bionano Solve is a set of tools for analyzing Bionano data False False +bioperl Converts GenBank format files to GFF3 False False +biotradis Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. True False +biscot Bionano scaffolding correction tool False False +bismark A tool to map bisulfite converted sequence reads and determine cytosine methylation states False False +blast2go Maps BLAST results to GO annotation terms True False +blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input False False +blast_plus_remote_blastp NCBI BLAST+ with -remote option False False +blast_rbh BLAST Reciprocal Best Hits (RBH) from two FASTA files True False +blast_to_scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs False False +blastparser_and_hits Parse blast outputs and compile hits False False +blastx_to_scaffold Generate DNA scaffold from blastx alignment of Contigs False False +blastxml_to_gapped_gff3 BlastXML to gapped GFF3 False False +blastxml_to_top_descr Make table of top BLAST match descriptions True False +blat_coverage_report Polymorphism of the Reads False False +blat_mapping Coverage of the Reads in wiggle format False False +blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. False False +blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. False False +blockclust BlockClust detects transcripts with similar processing patterns. False False +bracken Bayesian Reestimation of Abundance with KrakEN True False +braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . False False +braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . False False +brew3r_r Extend 3' end of a GTF using another GTF as a template +bumbershoot False False +bundle_collections Tool to bundle up list collection into a single zip to be download False False +busco BUSCO assess genome and annotation completeness True False +bwameth Fast and accurate alignment of BS-seq reads False False +cactus Cactus is a reference-free whole-genome multiple alignment program False False +calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. False False +calisp Calgary approach to isotopes in proteomics False False +cami_amber Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments +cap3 cap3 wrapper False False +cardinal Statistical and computational tools for analyzing mass spectrometry imaging datasets False False +cat Contig Annotation Tool (CAT) True False +cd_hit_dup simple tool for removing duplicates from sequencing reads True False +cdhit Cluster or compare biological sequence datasets True False +cell-types-analysis Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis False False +cemitool Gene co-expression network analysis tool True False +champ_blocs Compute indicators for turnover boulders fields False False +charts Enables advanced visualization options in Galaxy Charts False False +checkm Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes True False +checkv Assess quality of single-contig viral genomes +cherri Computational Help Evaluating RNA-RNA interactions False False +chipseeker A tool for ChIP peak annotation and visualization False False +chira Chimeric Read Annotator for RNA-RNA interactome data False False +chromeister ultra-fast pairwise genome comparisons False False +chromosome_diagram Chromosome Diagrams using Biopython False False +circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) False False +circexplorer2 Comprehensive and integrative circular RNA analysis toolset. False False +cite_seq_count Count CMO/HTO +clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling True False +clc_assembly_cell Galaxy wrapper for the CLC Assembly Cell suite from CLCBio False False +climate-stripes Create climate stripes from a tabular input file False False +clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins True False +clustalw ClustalW multiple sequence alignment program for DNA or proteins True False +cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. True False +cmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. False False +codeml Detects positive selection True False +cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. False False +cojac co-occurrence of mutations on amplicons True False +colabfold Protein prediction based on AlphaFold2 False False +colibread Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome False False +collapse_collection Collection tool that collapses a list of files into a single datasset in order of appears in collection False False +combineJSON JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. False False +combine_assembly_stats Combine multiple Assemblystats datasets into a single tabular report True False +combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances True False +combine_tabular_collection Combine Tabular Collection into a single file False False +compalignp Compute fractional identity between trusted alignment and test alignment False False +compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information True False +compleasm Compleasm: a faster and more accurate reimplementation of BUSCO True False +compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. False False +compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. False False +concoct CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. True False +consensus_from_alignments Tool to compute a consensus sequence from several aligned fasta sequences False False +consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment False False +coprarna Target prediction for prokaryotic trans-acting small RNAs False False +cosg Marker gene identification for single-cell sequencing data using COSG. +count_gff_features Count GFF Features False False +count_roi_variants Count sequence variants in region of interest in BAM file False False +coverage_report Generate Detailed Coverage Report from BAM file False False +coverage_stats BAM coverage statistics using samtools idxstats and depth False False +coverm CoverM genome and contig wrappers True False +crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. False False +crosscontamination_barcode_filter Barcode contamination discovery tool False False +crt CRISPR Recognition Tool False False +cryptogenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. True False +ctd_batch CTD analysis of chemicals, diseases, or genes False False +cummerbund Wrapper for the Bioconductor cummeRbund library False False +custom_pro_db CustomProDB False False +custom_pro_db_annotation_data_manager CustomProDB Annotation False False +cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). True False +dada2 DADA2 wrappers True False +das_tool DAS Tool for genome resolved metagenomics True False +data-hca Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects False False +data-scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home False False +data_exploration Explore data through multiple statistical tools False False +data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper False False +data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper False False +dbbuilder Protein Database Downloader False False +decontam Removes decontamination features (ASVs/OTUs) using control samples +decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. False False +deepsig Predictor of signal peptides in proteins based on deep learning False False +delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file False False +deseq2 Differential gene expression analysis based on the negative binomial distribution True False +deseq2_normalization Normalizes gene hitlists False False +dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data False False +dexseq Inference of differential exon usage in RNA-Seq False False +dia_umpire DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics False False +dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. False False +diamond DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. True False +diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. False False +diapysef diapysef is a convenience package for working with DIA-PASEF data False False +diffacto Diffacto comparative protein abundance estimation False False +disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler True False +divide_pg_snp Separate pgSnp alleles into columns False False +dorina data source for RNA interactions in post-transcriptional regulation False False +dose_responses A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses +dot2ct Dot-Bracket to Connect Table (CT) False False +dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence False False +dram DRAM for distilling microbial metabolism to automate the curation of microbiome function True False +drep dRep compares and dereplicates genome sets True False +droplet-barcode-plot Make a cell barcode plot for droplet single-cell RNA-seq QC False False +dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data False False +dropletutils De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 False False +ear A tool to compile assembly reports and stastics from assembly pipeline +ectyper EC-Typer - in silico serotyping of Escherichia coli species True False +edger Perform RNA-Seq differential expression analysis using edgeR pipeline False False +effectiveT3 Find bacterial type III effectors in protein sequences True False +eggnog_mapper eggnog-mapper fast functional annotation of novel sequences True False +egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing False False +emboss_5 Galaxy wrappers for EMBOSS version 5.0.0 tools True False +encyclopedia Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis False False +ete Analyse phylogenetic trees using the ETE Toolkit True False +evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. +exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data False False +exonerate Exonerate is a generic tool for pairwise sequence comparison. False False +exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. False False +export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn True False +express Quantify the abundances of a set of target sequences from sampled subsequences False False +ez_histograms ggplot2 histograms and density plots True False +falco A high throughput sequence QC analysis tool +fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) True False +fasta2bed Convert multiple fasta file into tabular bed file format False False +fasta_extract extract single fasta from multiple fasta file False False +fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) False False +fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. False False +fasta_stats Display summary statistics for a fasta file. False False +fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity True False +fastg2protlib Generate FASTA from FASTG False False +fastk FastK: A K-mer counter (for HQ assembly data sets) True False +fastp Fast all-in-one preprocessing for FASTQ files True False +fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) False False +fastq_pair_names Extract FASTQ paired read names False False +fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads False False +fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. False False +fastq_utils Set of tools for handling fastq files False False +fastqc_stats Summary multiple FastQC into a single tabular line report False False +fastqe FASTQE True False +fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL True False +feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy False False +featurecounter Feature coverage False False +featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome True False +feelnc Galaxy wrapper for FEELnc False False +feht Automatically identify makers predictive of groups. False False +fermikit FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. False False +fgsea Perform gene set testing using fgsea False False +filter_by_fasta_ids Filter FASTA on the headers and/or the sequences False False +filter_density Filter out position based on distance between SNVs False False +filter_spades_repeats Remove short and repeat contigs/scaffolds True False +filter_stats SNVPhyl filter_stats False False +filter_transcripts_via_tracking Filter Combined Transcripts False False +filter_vcf SNVPhyl filter_vcf False False +filtlong Filtlong - Filtering long reads by quality True False +find_diag_hits Find diagnostic hits False False +find_repeats Find repetitive regions on a reference genome using MUMMer False False +fisher_test Fisher's exact test on two-column hit lists. False False +flair FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. False False +flash Fast Length Adjustment of SHort reads False False +flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification True False +flye Assembly of long and error-prone reads. True False +format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels True False +fraggenescan Tool for finding (fragmented) genes in short read True False +fragpipe Data analysis for mass spectrometry-based proteomics. +freyja lineage abundances estimation True False +frogs Suite for metabarcoding analysis True False +funannotate Funannotate is a genome prediction, annotation, and comparison software package. True False +garnett De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 False False +gblocks Gblocks False False +gdal Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. False False +gecko Ungapped genome comparison False False +gemini GEMINI: a flexible framework for exploring genome variation False False +geneiobio Gene.iobio is an interactive tool for variant and trio analysis. False False +generate_pc_lda_matrix Generate a Matrix for using PC and LDA False False +genomad Identify virus and plasmid genomes from nucleotide sequences +genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases False False +get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) False False +getindelrates_3way Estimate Indel Rates for 3-way alignments False False +getindels_2way Fetch Indels from pairwise alignments False False +getmlst Download MLST datasets by species from pubmlst.org True False +getorganelle GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. False False +gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. False False +gff3_rebase Rebase a GFF against a parent GFF (e.g. an original genome) False False +gffread gffread filters and/or converts GFF3/GTF2 records False False +ggplot2 ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. True False +gi2taxonomy Fetch taxonomic representation True False +glimmer Glimmer makes gene predictions. True False +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) True False +gmaj GMAJ Multiple Alignment Viewer False False +goenrichment Performs GO Enrichment analysis. True False +goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data True False +gotohscan Find subsequences in db False False +graphclust GraphClust can be used for structural clustering of RNA sequences. False False +graphlan GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees True False +graphmap Mapper for long, error-prone reads. True False +graphprot GraphProt models binding preferences of RNA-binding proteins. False False +groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples +gsc_high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation False False +gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format +gtdbtk GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. True False +gtf-2-gene-list Utility to extract annotations from Ensembl GTF files. False False +gubbins Gubbins - bacterial recombination detection True False +guppy A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies False False +gwastools False False +hamronization Convert AMR gene detection tool output to hAMRonization specification format. True False +hansel Heidelberg and Enteritidis SNP Elucidation True False +hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies False False +hapog Hapo-G - Haplotype-Aware Polishing of Genomes False False +hardklor Hardklör False False +hcluster_sg Hierarchically clustering on a sparse graph False False +hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids False False +heatmap2 heatmap.2 function from the R gplots package False False +heinz An algorithm for identification of the optimal scoring subnetwork. False False +helixer Gene calling with Deep Neural Networks False False +hgv_fundo FunDO human genes associated with disease terms False False +hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve False False +hicexplorer HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. False False +hicstuff A toolkit to generate and manipulate Hi-C matrices False False +hifiasm A fast haplotype-resolved de novo assembler False False +hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. True False +high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps False False +hirondelle_crim_ogc_api_processes This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. +hisat HISAT is a fast and sensitive spliced alignment program. False False +hisat2 HISAT2 is a fast and sensitive spliced alignment program. False False +hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. True False +hmmer3 HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). True False +homer Software for motif discovery and next generation sequencing analysis. False False +homer HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. False False +htseq-clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets False False +htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) False False +humann HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution True False +hybpiper Analyse targeted sequence capture data False False +hyphy Hypothesis Testing using Phylogenies True False +hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies True False +icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. True False +idba_ud Wrappers for the idba assembler variants. True False +idconvert Convert mass spectrometry identification files on linux or MacOSX False False +idr Galaxy wrappers for the IDR package from Nathan Boleu False False +iedb_api Get epitope binding predictions from IEDB-API False False +illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays False False +improviser Visualisation of PepXML files False False +indels_3way Fetch Indels from 3-way alignments False False +infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." True False +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. False False +instagraal Large genome reassembly based on Hi-C data False False +instrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes True False +intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. False False +integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" True False +interpolation Run IDW interpolation based on a .csv and .geojson file False False +interproscan Interproscan queries the interpro database and provides annotations. True False +iphop Integrated Phage Host Prediction +iprscan5 Interproscan queries the interpro database and provides annotations. True False +iqtree Efficient phylogenomic software by maximum likelihood True False +isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" True False +isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. False False +isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments False False +itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. True False +ivar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing True False +jbrowse JBrowse Genome Browser integrated as a Galaxy Tool True False +jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool +jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) False False +jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA True False +kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. False False +kat_filter Filtering kmers or reads from a database of kmers hashes True False +kc-align Kc-Align custom tool True False +khmer In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more True False +kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. False False +kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) True False +kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model True False +kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. True False +kraken2 Kraken2 for taxonomic designation. True False +kraken2tax Convert Kraken output to Galaxy taxonomy data. True False +kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) True False +kraken_taxonomy_report Kraken taxonomy report True False +krakentools KrakenTools is a suite of scripts to be used alongside the Kraken True False +krocus Predict MLST directly from uncorrected long reads True False +labels remaps and annotates alignments False False +last LAST finds similar regions between sequences. False False +lca_wrapper Find lowest diagnostic rank True False +legsta Performs in silico Legionella pneumophila sequence based typing. True False +length_and_gc_content Gets gene length and gc content from a fasta and a GTF file False False +lfq_protein_quant Enable protein summarisation and quantitation False False +lighter Lighter is a kmer-based error correction method for whole genome sequencing data True False +limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline True False +lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) True False +links Scaffold genome assemblies with long reads. False False +locarna LocARNA - A suite for multiple alignment and folding of RNAs False False +logistic_regression_vif Perform Logistic Regression with vif False False +logol Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence False False +longorf obtain longest ORF in six-frame translations +lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) True False +lotus2 LotuS2 OTU processing pipeline True False +m6anet m6anet to detect m6A RNA modifications from nanopore data True False +maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. True False +macs2 MACS - Model-based Analysis of ChIP-Seq False False +maf_cpg_filter Mask CpG/non-CpG sites from MAF file False False +mafft Multiple alignment program for amino acid or nucleotide sequences True False +make_data_paper_sketches This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. +make_nr Make a FASTA file non-redundant True False +maker MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. True False +maldiquant MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. False False +map_peptides_to_bed Map peptides to a reference genome for display by a genome browser False False +mapping_quality_stats Collects and shows the distribution of MAPQ values in a BAM alignment file False False +mapping_to_ucsc Format mapping data as UCSC custom track False False +mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. True False +marine_omics The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data +mash Fast genome and metagenome distance estimation using MinHash True False +mashmap Fast local alignment boundaries False False +masigpro Identify significantly differential expression profiles in time-course microarray experiments False False +mauve_contig_mover Order a draft genome relative to a related reference genome False False +maxbin2 clusters metagenomic contigs into bins True False +maxquant wrapper for MaxQuant True False +mcl The Markov Cluster Algorithm, a cluster algorithm for graphs True False +mea Maximum expected accuracy prediction False False +mean-per-zone Creates a png image showing statistic over areas as defined in the vector file False False +medaka Sequence correction provided by ONT Research True False +medenv Retrieve environmental data from etopo, cmems and woa False False +megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. True False +megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) True False +megan MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). True False +meningotype Assign sequence type to N. meningitidis genome assemblies True False +merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. True False +meryl Meryl a k-mer counter. True False +meta_proteome_analyzer MetaProteomeAnalyzer False False +metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. True False +metabuli Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences +metaeuk MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. True False +metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage True False +metagenomeseq metagenomeSeq Normalization True False +metanovo Produce targeted databases for mass spectrometry analysis. True False +metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis True False +metaquantome quantitative analysis of microbiome taxonomy and function True False +metawrapmg A flexible pipeline for genome-resolved metagenomic data analysis True False +methtools tools for methylation analysis False False +methyldackel A tool for processing bisulfite sequencing alignments False False +metilene Differential DNA methylation calling False False +mg_toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. +mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. +miclip Identification of binding sites in CLIP-Seq data. False False +microsatbed Select microsatellites for a bed file +microsatellite_birthdeath Identify microsatellite births and deaths False False +microsats_alignment_level Extract Orthologous Microsatellites from pair-wise alignments False False +microsats_mutability Estimate microsatellite mutability by specified attributes False False +migmap mapper for full-length T- and B-cell repertoire sequencing False False +minced MinCED - Mining CRISPRs in Environmental Datasets False False +minia Short-read assembler based on a de Bruijn graph True False +miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) True False +minipolish Polishing miniasm assemblies True False +miniprot Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. True False +miranda Finds potential target sites for miRNAs in genomic sequences False False +mircounts Generates miRNA count lists from read alignments to mirBase. False False +mirmachine Tool to detect miRNA in genome sequences False False +mirnature Computational detection of canonical microRNAs False False +mitobim assemble mitochondrial genomes False False +mitohifi Assembly mitogenomes from Pacbio HiFi read. False False +mitos de-novo annotation of metazoan mitochondrial genomes True False +mlst Scan contig files against PubMLST typing schemes True False +moFF moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. False False +mob_suite MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies True False +monocle3 De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. False False +morpheus Morpheus MS Search Application False False +mothur Mothur wrappers True False +motus Tool for profiling the abundance of microbial taxa. +mqc Ribosome profiling mapping quality control tool False False +mqppep MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA False False +mrbayes A program for the Bayesian estimation of phylogeny. True False +msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container True False +msgfplus MSGF+ False False +msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. False False +msstats MSstats tool for analyzing mass spectrometry proteomic datasets False False +msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling True False +mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome False False +multigsea GSEA-based pathway enrichment analysis for multi-omics data True False +multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report True False +multispecies_orthologous_microsats Extract orthologous microsatellites False False +mummer Draw dotplots using mummer, mucmer, or promer with mummerplot False False +mummer4 Mummer4 Tools False False +mykrobe Antibiotic resistance predictions True False +mykrobe_parser RScript to parse the results of mykrobe predictor. True False +mz_to_sqlite Creates a SQLite database for proteomics data True False +mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. False False +naltorfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) False False +nanocompore Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. True False +nanoplot Plotting tool for long read sequencing data and alignments True False +nanopolishcomp NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. True False +nastiseq A method to identify cis-NATs using ssRNA-seq False False +ncbi_blast_plus NCBI BLAST+ True False +ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) +ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. False False +ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). True False +necat Error correction and de-novo assembly for ONT Nanopore reads False False +newick_utils Perform operations on Newick trees True False +nextclade Identify differences between your sequences and a reference sequence used by Nextstrain True False +nextdenovo String graph-based de novo assembler for long reads True False +nlstradamus Find nuclear localization signals (NLSs) in protein sequences False False +nonpareil Estimate average coverage in metagenomic datasets True False +novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. False False +nucleosome_prediction Prediction of Nucleosomes Positions on the Genome True False +nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. True False +oases Short read assembler False False +obisindicators Compute biodiveristy indicators for marine data from obis True False +obitools OBITools is a set of programs developed to simplify the manipulation of sequence files True False +ocean Access, process, visualise oceanographic data for the Earth System False False +odgi Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. False False +ogcProcess_otb_bandmath Outputs a monoband image which is the result of a mathematical operation on several multi-band images. False False +ogcProcess_otb_meanShiftSmoothing This application smooths an image using the MeanShift algorithm. False False +omark Proteome quality assessment software True False +ont_fast5_api ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. False False +openms OpenMS Suite for LC/MS data management and analyses False False +openms OpenMS in version 2.1. False False +optitype Precision HLA typing from NGS data False False +orfipy Galaxy wrapper for ORFIPY True False +orthofinder Accurate inference of orthologous gene groups made easy True False +pacu PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. +pairtools Flexible tools for Hi-C data processing False False +pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. False False +pangolin Phylogenetic Assignment of Named Global Outbreak LINeages False False +paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. False False +parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. False False +pathview Pathview is a tool set for pathway based data integration and visualization. False False +pathwaymatcher Reactome Pathway Matcher False False +patrist Extract Patristic Distance From a Tree False False +peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data False False +pep_pointer PepPointer categorizes peptides by their genomic coordinates. False False +pepquery A peptide-centric MS search engine for novel peptide identification and validation. False False +pepquery2 PepQuery2 peptide-centric MS search for peptide identification and validation False False +peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files False False +peptideshaker PeptideShaker and SearchGUI True False +peptimapper Proteogenomics workflow for the expert annotation of eukaryotic genomes False False +pepxml_to_xls Convert PepXML to Tabular False False +percolator Percolator False False +pfamscan Search a FASTA sequence against a library of Pfam HMM. True False +pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes True False +phyloseq Handling and analysis of high-throughput microbiome census data True False +phyml PhyML is a phylogeny software based on the maximum-likelihood principle. True False +pi_db_tools HiRIEF tools False False +picrust PICRUSt wrappers True False +picrust2 PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States True False +pipmir A method to identify novel plant miRNA. False False +piranha Piranha is a peak-caller for CLIP- and RIP-Seq data False False +plasflow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. True False +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler False False +plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" True False +plasmidspades Genome assembler for assemblying plasmid True False +platypus efficient and accurate variant-detection in high-throughput sequencing data False False +plotly_ml_performance_plots performance plots for machine learning problems False False +plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly False False +plotly_regression_performance_plots performance plots for regression problems False False +pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS False False +poisson2test Poisson two-sample test False False +polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" True False +predictnls Python reimplementation of predictNLS for Galaxy False False +presto pRESTO toolkit for immune repertoire analysis. False False +pretext Process genome contacts maps processing images. False False +prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets False False +probecoverage computes and plots read coverage of genomic regions by sequencing datasets False False +prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes True False +progressivemauve Mauve/ProgressiveMauve Multiple Sequence Aligner False False +prokka Rapid annotation of prokaryotic genomes True False +promer Aligns two sets of contigs and reports amino acid substitutions between them True False +prot-scriber Protein annotation of short human readable descriptions False False +protease_prediction This tool can learn the cleavage specificity of a given class of proteases. False False +protein_analysis TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb False False +protein_properties Calculation of various properties from given protein sequences False False +proteinortho Proteinortho is a tool to detect orthologous proteins/genes within different species. True False +proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. False False +proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. False False +proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. False False +proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. False False +proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. False False +proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. False False +proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. False False +proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. False False +proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. False False +proteore_venn_diagram ProteoRE JVenn Diagram False False +pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. False False +psm2sam PSM to SAM False False +psm_validation Validate PSM from Ion Fragmentation False False +psy-maps Visualization of regular geographical data on a map with psyplot False False +pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data False False +purge_dups Purge haplotigs and overlaps in an assembly based on read depth False False +pycoqc QC metrics for ONT Basecalling True False +pygenometracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. True False +pyprophet Semi-supervised learning and scoring of OpenSWATH results. False False +pyscenic PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ +pysradb pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. False False +pyteomics Tools using the pyteomics library False False +qiime_add_on QIIME to perform microbial community analysis True False +qiime_core QIIME to perform microbial community analysis True False +qiime_extract_viz Extract vizualization from QIIME artifacts +qq_tools False False +qualimap Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. True False +quality_filter Filter nucleotides based on quality scores False False +quantp Correlation between protein and transcript abundance False False +quantwiz_iq Isobaric Quantitation using QuantWiz-IQ False False +quasitools A collection of tools for analysing Viral Quasispecies False False +quast Quast (Quality ASsessment Tool) evaluates genome assemblies. True False +quickmerge Merge long-read and hybrid assemblies to increase contiguity True False +rRNA Identification of ribosomal RNA genes in metagenomic fragments. True False +racon Consensus module for raw de novo DNA assembly of long uncorrected reads. True False +ragtag Reference-guided scaffolding of draft genomes tool. False False +rapidnj Galaxy wrapper for the RapidNJ tool False False +rasusa Randomly subsample sequencing reads to a specified coverage True False +raven Raven is a de novo genome assembler for long uncorrected reads. False False +rawtools Raw Tools False False +raxml RAxML - A Maximum Likelihood based phylogenetic inference True False +rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs False False +rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments False False +rcve Compute RCVE False False +read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads True False +reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. True False +recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" True False +red Red (REpeat Detector) False False +refseq_masher Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. False False +regionalgam False False +remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation False False +repeat_masker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. False False +repeatexplorer2 Tool for annotation of repeats from unassembled shotgun reads. True False +repeatmasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. False False +repeatmodeler RepeatModeler - Model repetitive DNA False False +retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers +revoluzer revoluzer wrappers False False +ribotaper A method for defining traslated ORFs using Ribosome Profiling data. False False +ribowaltz Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data False False +rna_shapes Compute secondary structures of RNA False False +rnabob Fast pattern searching for RNA structural motifs False False +rnacode Analyze the protein coding potential in MSA False False +rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. False False +rnaformer RNAformer: RNA secondary structure prediction +rnalien RNAlien unsupervized RNA family model construction False False +rnaquast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. False False +rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs False False +rnaz RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. False False +roary Roary the pangenome pipeline True False +rsem transcript quantification from RNA-Seq data False False +rseqc an RNA-seq quality control package True False +ruvseq Remove Unwanted Variation from RNA-Seq Data False False +sailfish Sailfish is a tool for transcript quantification from RNA-seq data False False +salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. True False +salmon-kallisto-mtx-to-10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data False False +salsa2 A tool to scaffold long read assemblies with Hi-C False False +sample_seqs Sub-sample sequences files (e.g. to reduce coverage) False False +samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) False False +samtools_depth Coverage depth via samtools False False +samtools_idxstats BAM mapping statistics (using samtools idxstats) False False +sarscov2formatter sarscov2formatter custom script True False +sarscov2summary sarscov2summary custom script True False +sashimi_plot Generates a sashimi plot from bam files. False False +sc3 De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. False False +scanpy scanpy-scripts, command-line wrapper scripts around Scanpy. False False +scater De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. False False +scater Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. False False +schicexplorer scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. False False +scikit-bio scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics False False +scmap De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. False False +scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. True False +scpred De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 False False +sdmpredictors Terrestrial and marine predictors for species distribution modelling. False False +selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format False False +semibin SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks True False +seq2hla Precision HLA typing and expression from RNAseq data False False +seq_composition Sequence composition False False +seq_filter_by_id Filter sequences by ID False False +seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files False False +seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) False False +seq_primer_clip Trim off 5' or 3' primers False False +seq_rename Rename sequences with ID mapping from a tabular file False False +seq_select_by_id Select sequences by ID False False +seqcomplexity Sequence complexity for raw reads False False +seqkit A cross-platform and ultrafast toolkit for FASTA/Q file manipulation True False +seqprep Tool for merging paired-end Illumina reads and trimming adapters. True False +seqsero2 Salmonella serotype prediction from genome sequencing data True False +seqtk Toolkit for processing sequences in FASTA/Q formats False False +seqtk_nml Tool to downsample fastq reads False False +seqwish Alignment to variation graph inducer False False +seurat Seurat - R toolkit for single cell genomics False False +seurat De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 False False +shasta Fast de novo assembly of long read sequencing data False False +shorah Reconstruct haplotypes using ShoRAH in amplicon mode True False +short_reads_figure_high_quality_length Histogram of high quality score reads False False +short_reads_figure_score Build base quality distribution False False +shovill Faster de novo assembly pipeline based around Spades True False +sickle A windowed adaptive trimming tool for FASTQ files using quality False False +sina SINA reference based multiple sequence alignment False False +sistr_cmd SISTR in silico serotyping tool True False +sixgill Six-frame Genome-Inferred Libraries for LC-MS/MS False False +slamdunk Slamdunk maps and quantifies SLAMseq reads False False +sleuth Sleuth is a program for differential analysis of RNA-Seq data. False False +small_rna_clusters clusters small rna reads in alignment BAM files False False +small_rna_maps Generates small read maps from alignment BAM files False False +small_rna_signatures Computes the tendency of small RNAs to overlap with each other. False False +smallgenomeutilities Set of utilities for manipulating small viral genome data. True False +smalt SMALT aligns DNA sequencing reads with a reference genome. True False +smart_domains SMART domains False False +smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing False False +snap SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. True False +sniffles Galaxy wrapper for sniffles False False +snipit Summarise snps relative to a reference sequence False False +snippy Contains the snippy tool for characterising microbial snps True False +snv_matrix Generate matrix of SNV distances False False +socru Order and orientation of complete bacterial genomes False False +sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. True False +sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. True False +spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. True False +spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. False False +spapros Select and evaluate probe sets for targeted spatial transcriptomics. +spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. False False +spectrast2spectrast_irt Filter from spectraST files to swath input files False False +spectrast2tsv Filter from spectraST files to swath input files False False +spocc Get species occurences data False False +spolpred A program for predicting the spoligotype from raw sequence reads False False +spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads True False +sr_bowtie bowtie wrapper tool to align small RNA sequencing reads True False +sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. False False +srs_tools Compute biodiversity indicators for remote sensing data from Sentinel 2 False False +srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens True False +srst2 Short Read Sequence Typing for Bacterial Pathogens True False +sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data False False +stacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq False False +stacks2 Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq False False +star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR False False +staramr Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. True False +stoc Tools to analyse STOC data. False False +stringmlst Rapid and accurate identification of the sequence type (ST) True False +structure for using multi-locus genotype data to investigate population structure. True False +structureharvester for parsing STRUCTURE outputs and for performing the Evanno method False False +substitution_rates Estimate substitution rates for non-coding regions False False +substitutions Fetch substitutions from pairwise alignments False False +suite_qiime2__alignment True False +suite_qiime2__composition True False +suite_qiime2__cutadapt True False +suite_qiime2__dada2 True False +suite_qiime2__deblur True False +suite_qiime2__demux True False +suite_qiime2__diversity True False +suite_qiime2__diversity_lib True False +suite_qiime2__emperor True False +suite_qiime2__feature_classifier True False +suite_qiime2__feature_table True False +suite_qiime2__fragment_insertion True False +suite_qiime2__longitudinal True False +suite_qiime2__metadata True False +suite_qiime2__phylogeny True False +suite_qiime2__quality_control True False +suite_qiime2__quality_filter True False +suite_qiime2__rescript True False +suite_qiime2__sample_classifier True False +suite_qiime2__taxa True False +suite_qiime2__vsearch True False +suite_qiime2_core True False +suite_qiime2_core__tools True False +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl False False +syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. False False +t2ps Draw phylogeny True False +t2t_report Summarize taxonomy True False +t_coffee T-Coffee True False +tapscan Search for transcription associated proteins (TAPs) False False +tarfast5 produces a tar.gz archive of fast5 sequence files False False +targetfinder Plant small RNA target prediction tool False False +tasmanian_mismatch Analysis of positional mismatches False False +taxonkit TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit +taxonomy_filter_refseq Filter RefSeq by taxonomy False False +taxonomy_krona_chart Krona pie chart from taxonomic profile True False +taxpasta standardise taxonomic profiles +tb-profiler Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. True False +tbl2gff3 Table to GFF3 False False +te_finder Transposable element insertions finder False False +telescope Single locus resolution of Transposable ELEment expression. False False +tetoolkit The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. False False +tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. False False +tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. False False +tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. +tn93 Compute distances between sequences False False +tooldistillator ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files True False +tophat Tophat for Illumina False False +tophat2 Tophat - fast splice junction mapper for RNA-Seq reads False False +transdecoder TransDecoder finds coding regions within transcripts False False +transit TRANSIT True False +translate_bed Translate BED transcript CDS or cDNA in 3 frames False False +translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column False False +transtermhp Finds rho-independent transcription terminators in bacterial genomes True False +trim_galore Trim Galore adaptive quality and adapter trimmer True False +trinity Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq False False +trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. False False +trna_prediction Aragorn predicts tRNA and tmRNA in nucleotide sequences. False False +trycycler Trycycler toolkit wrappers True False +tsebra This tool has been developed to combine BRAKER predictions. False False +ucsc_axtchain Chain together genome alignments +ucsc_blat Standalone blat sequence search command line tool False False +ucsc_chainnet Make alignment nets out of chains +ucsc_chainprenet Remove chains that don't have a chance of being netted +ucsc_chainsort Sort chains. By default sorts by score. +ucsc_custom_track Build custom track for UCSC genome browser False False +ucsc_netfilter Filter out parts of net +ucsc_netsyntenic Add synteny info to a net dataset +umi_tools UMI-tools extract - Extract UMIs from fastq False False +unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. True False +unipept Unipept retrieves metaproteomics information True False +uniprot_rest_interface UniProt ID mapping and sequence retrieval False False +uniprotxml_downloader Download UniProt proteome in XML or fasta format True False +usher UShER toolkit wrappers True False +valet A pipeline for detecting mis-assemblies in metagenomic assemblies. True False +validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. False False +vapor Classify Influenza samples from raw short read sequence data True False +varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses True False +vcf2snvalignment Generates multiple alignment of variant calls False False +vegan an R package fo community ecologist True False +velvet de novo genomic assembler specially designed for short read sequencing technologies True False +velvet_optimiser Automatically optimize Velvet assemblies True False +venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc False False +verify_map Checks the mapping quality of all BAM(s) False False +verkko Telomere-to-telomere assembly pipeline False False +vg Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods False False +vibrant Virus Identification By iteRative ANnoTation +vienna_rna ViennaRNA - Prediction and comparison of RNA secondary structures False False +vigiechiro Tools created by the vigiechiro team to analyses and identify chiro sounds files. False False +virAnnot virAnnot wrappers True False +virheat generates a heatmap of allele frequencies from vcf files +virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. +volcanoplot Tool to create a Volcano Plot False False +vsearch VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. True False +vsnp The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. False False +vt A tool set for short variant discovery in genetic sequence data. False False +wade identify regions of interest False False +weather_app provides simple weather in text format False False +weightedaverage Assign weighted-average of the values of features overlapping an interval False False +windowmasker Identify repetitive regions using WindowMasker False False +windowsplitter Make windows False False +wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. True False +xarray xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. False False +xpore Identification and quantification of differential RNA modifications from direct RNA sequencing False False +yac_clipper Clips 3' adapters for small RNA sequencing reads. False False +yahs Yet Another Hi-C scaffolding tool False False +zeiss_lmd_converter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems +zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. 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ExpandNameSourceIDLinkCreatorsTagsCreation timeUpdate timeLatest versionVersionsNumber of stepsToolsEDAM operationsEDAM topicsLicenseDOI
bacterial-genome-assembly/mainWorkflowHub1043https://workflowhub.eu/workflows/1043?version=5Abromics None, Pierre Marin, Clea SiguretABRomics, Assembly, FASTQ, Genomics, bacterial-genomics, paired-end, quality2024-10-072024-10-07557.0refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillatorGenome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, VisualisationGPL-3.0-or-later
quality-and-contamination-control/mainWorkflowHub1052https://workflowhub.eu/workflows/1052?version=6ABRomics None, Pierre Marin, Clea SiguretABRomics, FASTQ, Genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming2024-10-122024-10-12666.0recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillatorParsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classificationGPL-3.0-or-later
Training: 16S rRNA Sequencing With Mothur: Main Tutorialhttps://usegalaxy.euf21d6a40a10a8ae8https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8microbiome2024-09-302024-10-0111mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_remove_groups, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_seq_error, mothur_tree_shared, mothur_cluster, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_get_groups, mothur_summary_single, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearchSequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding
MGnify amplicon summary tableshttps://usegalaxy.eu05dc8f4321a42cdchttps://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdcRand ZoabiMGnify_Amplicon, amplicon, metagenomics2024-05-222024-09-276868tp_awk_tool, query_tabular, collection_column_join, Grouping1, filter_tabularMIT
virannot_post_CLChttps://usegalaxy.eu86465932556bc96chttps://usegalaxy.eu/published/workflow?id=86465932556bc96cMarie Lefebvrevirology, otu, virannot, RPS, virus2024-08-212024-09-2666taxonomy_krona_chart, virannot_blast2tsv, ncbi_tblastx_wrapper, virAnnot_rps2tsv, krona-text, ncbi_rpstblastn_wrapper, virannot_otuSequence clustering, Sequence cluster visualisation, Sequence annotation, Visualisation
bacterial_genome_annotation (release v1.1.4)https://usegalaxy.eud8db0b2e30370b84https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-262024-09-2611integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
Bacterial Genome Assembly using Shov (release v1.1.2)https://usegalaxy.eu723e718f37e9ab91https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91abromics-consortium, ABRomics, Pierre Marin, Clea Siguretfastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics2024-09-262024-09-2611refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillatorGenome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, VisualisationGPL-3.0-or-later
amr_gene_detection (release v1.1.2)https://usegalaxy.eue37cc0b64774561bhttps://usegalaxy.eu/published/workflow?id=e37cc0b64774561bABRomics, abromics-consortium, Pierre Marin, Clea Siguretfasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection2024-09-262024-09-2611amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillatorParsing, Antimicrobial resistance prediction, Data handlingGPL-3.0-or-later
Taxonomy Profiling and Visualization with Kron (release v0.1)https://usegalaxy.euad8b6d73c9654305https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305Engy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2024-09-192024-09-1911kraken2, taxonomy_krona_chart, krakentools_kreport2kronaTaxonomic classification, Aggregation, VisualisationMIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1)https://usegalaxy.euf6a763951d815944https://usegalaxy.eu/published/workflow?id=f6a763951d815944Engy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2024-09-192024-09-1911clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods)MIT
Nanopore Preprocessing (release v0.1)https://usegalaxy.eu344cd3a3c2ce5302https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302Bérénice Batut, Engy Nasr, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, name:IWC2024-09-192024-09-1911Cut1, samtools_fastx, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, Grep1, collection_column_join, multiqc, porechop, nanoplot, Add_a_column1, fastqc, kraken2, fastp, collapse_dataset, minimap2, bamtools_split_mappedAggregation, Sequence composition calculation, Data handling, Validation, Statistical calculation, Visualisation, Sequence alignment analysis, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Taxonomic classification, Scatter plot plottingMIT
Gene-based Pathogen Identification (release v0.1)https://usegalaxy.eu77e5bbd317750915https://usegalaxy.eu/published/workflow?id=77e5bbd317750915Engy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:PathoGFAIR, name:IWC, name:microGalaxy2024-09-192024-09-1911param_value_from_file, bandage_image, medaka_consensus_pipeline, collection_element_identifiers, abricate, split_file_to_collection, tab2fasta, compose_text_param, tp_find_and_replace, __BUILD_LIST__, flye, fasta2tabMapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assemblyMIT
Allele-based Pathogen Identification (release v0.1)https://usegalaxy.eud215a2e554fd83bchttps://usegalaxy.eu/published/workflow?id=d215a2e554fd83bcEngy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2024-09-192024-09-1911Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depthVariant calling, Pairwise sequence alignmentMIT
Allele-based Pathogen Identification (release v0.1.1)https://usegalaxy.eucdf2f02428f5f83fhttps://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83fEngy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2024-09-192024-09-1911Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depthVariant calling, Pairwise sequence alignmentMIT
bacterial_genome_annotation (release v1.0)https://usegalaxy.eu61948fcaefa1418ahttps://usegalaxy.eu/published/workflow?id=61948fcaefa1418aABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-192024-09-1911integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
bacterial_genome_annotation (release v1.1)https://usegalaxy.eu8792eaecb69fbc26https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-192024-09-1911integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
bacterial_genome_annotation (release v1.1.1)https://usegalaxy.eu36ea584e0f60893ehttps://usegalaxy.eu/published/workflow?id=36ea584e0f60893eABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-192024-09-1911integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
bacterial_genome_annotation (release v1.1.2)https://usegalaxy.eubcd50e655809cfcbhttps://usegalaxy.eu/published/workflow?id=bcd50e655809cfcbABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-192024-09-1911integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
bacterial_genome_annotation (release v1.1.3)https://usegalaxy.eu4a218fb93d78ba67https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation2024-09-192024-09-1911integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescanParsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognitionGPL-3.0-or-later
Quality and Contamination Control For Genome Assembly (release v1.0)https://usegalaxy.eu884a4415b669690chttps://usegalaxy.eu/published/workflow?id=884a4415b669690cABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming2024-09-192024-09-1911recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillatorParsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classificationGPL-3.0-or-later
Quality and Contamination Control For Genome Assembly (release v1.1)https://usegalaxy.euaafcfcb585c5ca75https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming2024-09-192024-09-1911recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillatorParsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classificationGPL-3.0-or-later
Quality and Contamination Control For Genome Assembly (release v1.1.1)https://usegalaxy.eu0c47571d20535426https://usegalaxy.eu/published/workflow?id=0c47571d20535426ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming2024-09-192024-09-1911recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillatorParsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classificationGPL-3.0-or-later
Quality and Contamination Control For Genome Assembly (release v1.1.2)https://usegalaxy.eu0a82eb8b44d9d502https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502ABRomics, abromics-consortium, Pierre Marin, Clea SiguretGenomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming2024-09-192024-09-1911recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillatorParsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classificationGPL-3.0-or-later
Bacterial Genome Assembly using Shov (release v1.0)https://usegalaxy.eu3d937648809ca4e7https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7abromics-consortium, Abromics, Pierre Marin, Clea Siguretfastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics2024-09-192024-09-1911refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillatorGenome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, VisualisationGPL-3.0-or-later
Bacterial Genome Assembly using Shov (release v1.1)https://usegalaxy.eufca458178b3c794ahttps://usegalaxy.eu/published/workflow?id=fca458178b3c794aabromics-consortium, ABRomics, Pierre Marin, Clea Siguretfastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics2024-09-192024-09-1911refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillatorGenome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, VisualisationGPL-3.0-or-later
Bacterial Genome Assembly using Shov (release v1.1.1)https://usegalaxy.eu4216424f032c055fhttps://usegalaxy.eu/published/workflow?id=4216424f032c055fabromics-consortium, ABRomics, Pierre Marin, Clea Siguretfastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics2024-09-192024-09-1911refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillatorGenome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, VisualisationGPL-3.0-or-later
amr_gene_detection (release v1.0)https://usegalaxy.eu41d207d06a32ba05https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05ABRomics, abromics-consortium, Pierre Marin, Clea Siguretfasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection2024-09-192024-09-1911amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillatorParsing, Antimicrobial resistance prediction, Data handlingGPL-3.0-or-later
amr_gene_detection (release v1.1)https://usegalaxy.euabe85758e77c78e6https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6ABRomics, abromics-consortium, Pierre Marin, Clea Siguretfasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection2024-09-192024-09-1911amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillatorParsing, Antimicrobial resistance prediction, Data handlingGPL-3.0-or-later
amr_gene_detection (release v1.1.1)https://usegalaxy.euf30f8e7dcd50cd0dhttps://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0dABRomics, abromics-consortium, Pierre Marin, Clea Siguretfasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection2024-09-192024-09-1911amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillatorParsing, Antimicrobial resistance prediction, Data handlingGPL-3.0-or-later
dada2 amplicon analysis pipeline - for paired en (release v0.2)https://usegalaxy.eu642f4c47028031d7https://usegalaxy.eu/published/workflow?id=642f4c47028031d7Matthias Bernt, UFZ Leipzigname:amplicon2024-09-192024-09-1911dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCountsVariant calling, DNA barcodingMIT
Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.2)https://usegalaxy.eu6e1fe7372e93fae0https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0Viktoria Isabel Schwarz, Wolfgang Maierpox, virology2024-09-192024-09-1911ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignmentMIT
LŠMB: Identification of the micro-organisms in a beer using Nanopore sequencinghttps://usegalaxy.eu181e751be8dd9abchttps://usegalaxy.eu/published/workflow?id=181e751be8dd9abcBérénice Batut, Teresa Müller, Polina PoluninaMicrobiome2024-09-082024-09-0800taxonomy_krona_chart, Filter1, porechop, nanoplot, fastqc, kraken2, fastp, krakentools_kreport2kronaAggregation, Sequence composition calculation, Statistical calculation, Visualisation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plottingMIT
MGnify's amplicon pipeline v5.0 - Quality control SEhttps://usegalaxy.eub7166aff73e5d81chttps://usegalaxy.eu/published/workflow?id=b7166aff73e5d81cMGnify - EMBL, Rand Zoabi, Paul ZierepMGnify_Amplicon, amplicon, metagenomics2024-03-252024-08-211313trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, prinseq, fastqc, tp_find_and_replace, fastq_filterSequence composition calculation, Sequence trimming, Sequence contamination filtering, Sequencing quality control, Statistical calculation, Validation, Read pre-processingApache-2.0
MGnify's amplicon pipeline v5.0 - ITShttps://usegalaxy.eu169327ba670607d1https://usegalaxy.eu/published/workflow?id=169327ba670607d1EMBL's European Bioinformatics Institute, Rand Zoabi, Paul ZierepMGnify_Amplicon, amplicon, metagenomics2024-05-062024-08-212323__FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, __FILTER_EMPTY_DATASETS__, collection_element_identifiers, biom_convert, mapseq, bedtools_maskfastabedMapping, Formatting, Visualisation, k-mer countingApache-2.0
MGnify's amplicon pipeline v5.0 - Quality control PEhttps://usegalaxy.euf9648091c06171cdhttps://usegalaxy.eu/published/workflow?id=f9648091c06171cdEMBL's European Bioinformatics Institute, Rand Zoabi, Paul ZierepMGnify_Amplicon, amplicon, metagenomics2024-05-272024-08-211414__UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, fastq_filter, prinseq, mgnify_seqprep, fastqc, tp_find_and_replace, fastpSequence composition calculation, Validation, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence trimmingApache-2.0
MGnify's amplicon pipeline v5.0 - rRNA predictionhttps://usegalaxy.eu0c3eee883f5ab977https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977EMBL's European Bioinformatics Institute, Rand Zoabi, Paul ZierepMGnify_Amplicon, metagenomics, amplicon2024-05-062024-08-212929__FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, query_tabular, __FILTER_EMPTY_DATASETS__, cmsearch_deoverlap, collection_element_identifiers, gops_concat_1, cshl_fasta_formatter, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseqFormatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, VisualisationApache-2.0
MGnify's amplicon pipeline v5.0 - completehttps://usegalaxy.eu02f90a96d01fed4fhttps://usegalaxy.eu/published/workflow?id=02f90a96d01fed4fEMBL's European Bioinformatics Institute, Rand Zoabi, Paul ZierepMGnify_Amplicon, metagenomics, amplicon2024-05-062024-08-217979fasterq_dump, __MERGE_COLLECTION__Data handlingApache-2.0
pAllori Amplicon 16S Pre-Processing and Taxonomy Classificationhttps://usegalaxy.eu466bdd8ba7b67264https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264Engy Nasr, Paul Zierepname:microGalaxy, name:16s, name:metagenomics, name:pallori2023-06-302024-08-136969lotus2, taxonomy_krona_chart, ampvis2_load, __FLATTEN__, trimmomatic, collection_column_join, multiqc, ampvis2_ordinate, cutadapt, unzip, fastqc, kraken2, tp_cut_tool, krakentools_kreport2krona, ampvis2_heatmapAggregation, Sequence composition calculation, Sequence trimming, Sequence feature detection, Validation, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Analysis, Sequencing quality control, Taxonomic classification, DNA barcodingMIT
Capripox isolate subtyping and consensus genome generation from WGS datahttps://usegalaxy.eu629e57958afed44chttps://usegalaxy.eu/published/workflow?id=629e57958afed44cWolfgang MaierCaPV, VETLAB, virology2024-07-282024-08-0299param_value_from_file, fasta_regex_finder, __FLATTEN__, qualimap_bamqc, ivar_consensus, __FILTER_FAILED_DATASETS__, bwa_mem, Show beginning1, read_it_and_keep, samtools_view, multiqc, tp_find_and_replace, fastp, collapse_dataset, __EXTRACT_DATASET__, vaporGeneration, Data retrieval, Validation, Genome indexing, Sequence alignment, Filtering, Genome alignment, Sequence contamination filtering, Sequencing quality control, De-novo assembly, Read mappingAGPL-3.0-or-later
Pox Virus Illumina Amplicon Workflow from half-genomeshttps://usegalaxy.eua31100610fba17a1https://usegalaxy.eu/published/workflow?id=a31100610fba17a1Viktoria Isabel Schwarz, Wolfgang Maierpox, virology2024-08-022024-08-0200ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignmentMIT
pAllori Blood RNAhttps://usegalaxy.euca9d3233b0912765https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765Engy Nasr, Paul Zierepname:microGalaxy, name:pallori, name:BloodRNA, name:UMI, name:Barcode, name:transcriptomics2023-07-022024-07-293737umi_tools_extract, __FLATTEN__, featurecounts, __FILTER_FAILED_DATASETS__, collection_column_join, multiqc, fastqc, rna_starValidation, Sequence composition calculation, Statistical calculation, Sequencing quality control, Read summarisation, Sequence alignment, RNA-Seq quantificationMIT
pAllori WGShttps://usegalaxy.eu4f245ac304ab76d9https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9Engy Nasr, Paul Zierepname:pallori, name:microGalaxy, name:WGS2024-07-162024-07-281616freebayes, Remove beginning1, ggplot2_heatmap, bowtie2, __FLATTEN__, vcf2tsv, tp_awk_tool, regexColumn1, abricate, trimmomatic, collection_column_join, multiqc, Grouping1, fastqc, snpSift_filter, shovill, bcftools_norm, bcftools_viewSequence composition calculation, Variant calling, Validation, Statistical calculation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Sequencing quality control, Read mappingMIT
Influenza sequence data analysishttps://usegalaxy.eubc5ced57e711acf9https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9Wolfgang Maier, Viktoria Isabel SchwarzAIV, VETLAB, virology2024-07-262024-07-282121map_param_value, iqtree, qualimap_bamqc, seqtk_subseq, bwa_mem, Show beginning1, __RELABEL_FROM_FILE__, snipit, collapse_dataset, Grep1, tp_find_and_replace, rbc_mafft, __EXTRACT_DATASET__, vapor, __APPLY_RULES__, ivar_consensus, __UNZIP_COLLECTION__, bamtools_split_ref, Paste1, __DUPLICATE_FILE_TO_COLLECTION__, pick_value, fastp, param_value_from_file, collection_element_identifiers, samtools_view, wc_gnuGeneration, De-novo assembly, Data retrieval, Data handling, Phylogenetic analysis, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence file editing, Sequence contamination filtering, Sequencing quality control, Base position variability plotting, Sequence analysis, Read mapping, Multiple sequence alignmentAGPL-3.0-or-later
MAGs workflowhttps://usegalaxy.eu97312d273b6e8bd9https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9name:microGalaxy2023-11-152024-07-111414Fasta_to_Contig2Bin, samtools_sort, metabat2_jgi_summarize_bam_contig_depths, megahit, fastq_paired_end_interlacer, semibin, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_coverage_table, coverm_genome, bowtie2, __UNZIP_COLLECTION__, das_tool, metabat2, quast, checkm_lineage_wf, concoct_merge_cut_up_clustering, concoct, drep_dereplicate, maxbin2Sequence clustering, Sequence composition calculation, Read binning, Sequence assembly validation, Sequence assembly, Statistical calculation, Validation, Visualisation, Genome comparison, Genome assembly, Local alignment, Sequencing quality control, Genome annotation, Read mapping
PathoGFAIRhttps://usegalaxy.eu0dce37adb369492chttps://usegalaxy.eu/published/workflow?id=0dce37adb369492cEngy Nasr, Bérénice Batut, Paul Zierepname:microGalaxy, name:IWC, name:PathoGFAIR, name:Nanopore, name:Collection2024-05-312024-07-039393MIT
Pathogen Detection PathoGFAIR Samples Aggregation and Visualisationhttps://usegalaxy.eu376119528377a3aehttps://usegalaxy.eu/published/workflow?id=376119528377a3aeEngy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2024-04-032024-06-245858clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods)MIT
Allele-based Pathogen Identificationhttps://usegalaxy.eu09c7069ae409c362https://usegalaxy.eu/published/workflow?id=09c7069ae409c362Engy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2023-04-122024-06-247272Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depthVariant calling, Pairwise sequence alignmentMIT
Nanopore Preprocessinghttps://usegalaxy.eua705370bc2c13d5chttps://usegalaxy.eu/published/workflow?id=a705370bc2c13d5cBérénice Batut, Engy Nasr, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, name:IWC2023-04-122024-06-24190190Cut1, samtools_fastx, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, Grep1, collection_column_join, multiqc, porechop, nanoplot, Add_a_column1, fastqc, kraken2, fastp, collapse_dataset, minimap2, bamtools_split_mappedAggregation, Sequence composition calculation, Data handling, Validation, Statistical calculation, Visualisation, Sequence alignment analysis, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Taxonomic classification, Scatter plot plottingMIT
Taxonomy Profiling and Visualization with Phinchhttps://usegalaxy.eub67b5ecd3305f830https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830Engy Nasr, Bérénice Batut, Paul Zierepname:collection, name:microGalaxy, name:GTN2023-04-122024-06-1988kraken2, interactive_tool_phinch, kraken_biomTaxonomic classificationMIT
metaQuantome_datacreation_workflowhttps://usegalaxy.eufc42cc9467c6ee8dhttps://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8dproteomics, name:microGalaxy2023-12-142024-06-1900Cut1, Remove beginning1, flashlfq, regex1, query_tabular, Filter1, msconvert, tp_replace_in_line, tp_replace_in_column, search_gui, peptide_shaker, unipeptFiltering, Prediction and recognition, Label-free quantification, Formatting, Visualisation
QIIME2 I: Demultiplexing (single-end)https://usegalaxy.eu86b31ac8a7720e41https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZname:amplicon, name:16S, name:tutorial2024-06-122024-06-1811qiime2_core__tools__import, qiime2__demux__summarize, qiime2__demux__emp_singleMIT
QIIME2 II: Denoising (sequence quality control) and feature table creation (single-end)https://usegalaxy.euda17a4d690eb0ff3https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZname:amplicon, name:16S, name:tutorial2024-06-122024-06-1811qiime2__feature_table__tabulate_seqs, qiime2__feature_table__summarize, qiime2__metadata__tabulate, qiime2__dada2__denoise_singleMIT
Gene-based Pathogen Identificationhttps://usegalaxy.eu585c21b7b1d864fchttps://usegalaxy.eu/published/workflow?id=585c21b7b1d864fcEngy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:PathoGFAIR, name:IWC, name:microGalaxy2023-04-132024-06-05142142param_value_from_file, bandage_image, medaka_consensus_pipeline, collection_element_identifiers, abricate, split_file_to_collection, tab2fasta, compose_text_param, tp_find_and_replace, __BUILD_LIST__, flye, fasta2tabMapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assemblyMIT
Taxonomy Profiling and Visualization with Kronahttps://usegalaxy.eu10101558b211a782https://usegalaxy.eu/published/workflow?id=10101558b211a782Engy Nasr, Bérénice Batut, Paul Zierepname:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC2023-05-112024-06-055858kraken2, taxonomy_krona_chart, krakentools_kreport2kronaTaxonomic classification, Aggregation, VisualisationMIT
FASTQC-MULTIQC-Quality-Check_FastQ_Fileshttps://usegalaxy.eu0ec684b341ad172dhttps://usegalaxy.eu/published/workflow?id=0ec684b341ad172dBGGM, Microbiome, Amplicon, FASTQC, QualityCheck2024-05-132024-05-1788multiqc, fastqcSequence composition calculation, Sequencing quality control, Validation, Statistical calculation
Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptoolhttps://usegalaxy.euc8bc4af6dd3b5d02https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02Engy Nasr, Bérénice Batutmicrobiome, nanopore, IWC, name:Collection, name:microGalaxy2022-11-292024-04-04205205clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, interactive_tool_jupyter_notebook, __FILTER_FAILED_DATASETS__Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods)MIT
Mgnify MLhttps://usegalaxy.eu011f701c5a55bfdfhttps://usegalaxy.eu/published/workflow?id=011f701c5a55bfdfname:microGalaxy2023-10-102024-03-15128128__BUILD_LIST__, interactive_tool_jupyter_notebook
dada2 amplicon analysis pipeline - for paired en (release v0.1)https://usegalaxy.eub483cf6a138d2372https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372Matthias Bernt, UFZ Leipzigname:amplicon2024-03-142024-03-1411dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCountsVariant calling, DNA barcodingMIT
Normalizationhttps://usegalaxy.eu0603f0898211f806https://usegalaxy.eu/published/workflow?id=0603f0898211f806name:microGalaxy2023-09-252024-03-138080map_param_value, __FILTER_EMPTY_DATASETS__, Grep1, __BUILD_LIST__, __EXTRACT_DATASET__
WF1_Database_Generation_Workflowhttps://usegalaxy.eu7cfbf4b7bd3f30d3https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3name:clinicalMP, name:microGalaxy2023-12-142023-12-1411metanovo, fasta_merge_files_and_filter_unique_sequencesTag-based peptide identification, Target-Decoy, de Novo sequencing, Protein identification, Expression analysis
WF2_Discovery-Workflowhttps://usegalaxy.eu8af41219411062adhttps://usegalaxy.eu/published/workflow?id=8af41219411062adname:microGalaxy, name:clinicalMP2023-12-142023-12-1411Cut1, dbbuilder, Remove beginning1, tp_cat, query_tabular, Filter1, peptide_shaker, msconvert, Grep1, Grouping1, filter_tabular, maxquant, ident_params, search_gui, fasta_cli, fasta_merge_files_and_filter_unique_sequences, fasta2tabHeat map generation, Statistical calculation, Visualisation, Protein quantification, Filtering, Principal component plotting, Formatting, Standardisation and normalisation, Imputation, Clustering
WF3_VERIFICATION_WORKFLOWhttps://usegalaxy.eud87fc6685e47d27dhttps://usegalaxy.eu/published/workflow?id=d87fc6685e47d27dname:microGalaxy, name:clinicalMP2023-12-142023-12-1411Cut1, dbbuilder, Remove beginning1, tp_cat, pepquery2, query_tabular, Filter1, Grouping1, uniprotxml_downloader, collapse_dataset, fasta_merge_files_and_filter_unique_sequences
WF4_Quantitation_Workflowhttps://usegalaxy.eua49275eb8b2b2ecbhttps://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecbname:clinicalMP, name:microGalaxy2023-12-142023-12-1411Cut1, maxquant, Grep1, Grouping1Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering
WF5_Data_Interpretation_Worklowhttps://usegalaxy.eu755ede37d94dc456https://usegalaxy.eu/published/workflow?id=755ede37d94dc456name:microGalaxy, name:clinicalMP2023-12-142023-12-1411Grep1, msstatstmt, unipeptPrediction and recognition, Visualisation
MetaG_extendedhttps://usegalaxy.eud57d41e306241396https://usegalaxy.eu/published/workflow?id=d57d41e306241396name:microgalaxy2023-12-142023-12-1411coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wfData retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction
MetaPhttps://usegalaxy.eu01ac8bf9832789e2https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2name:microgalaxy2023-12-142023-12-1411maxquantHeat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering
MetaThttps://usegalaxy.eu3733bcdf5b458be7https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7name:microgalaxy2023-12-142023-12-1411kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqcSequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling
metaquantome-taxonomy-workflowhttps://usegalaxy.eu695f7defb516d80dhttps://usegalaxy.eu/published/workflow?id=695f7defb516d80dproteomics, name:microGalaxy2023-12-142023-12-1400metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_statQuery and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification
metaquantome-function-worklowhttps://usegalaxy.eu4c364c6be27981bahttps://usegalaxy.eu/published/workflow?id=4c364c6be27981baproteomics, name:microGalaxy2023-12-142023-12-1400metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_statQuery and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification
Metaproteomics_GTNhttps://usegalaxy.eu68967c922de149aehttps://usegalaxy.eu/published/workflow?id=68967c922de149aeproteomics, name:microGalaxy2023-12-142023-12-1400query_tabular, sqlite_to_tabular, search_gui, peptide_shaker, unipeptPrediction and recognition, Visualisation
Ecoli Comparisonhttps://usegalaxy.eu0e492839192d26e0https://usegalaxy.eu/published/workflow?id=0e492839192d26e0assembly, name:microGalaxy2023-12-142023-12-1400tp_grep_tool, collapse_dataset, lastz_wrapper_2, join1, mergeCols1, bedtools_complementbed, tp_sed_tool, Grep1, bedtools_intersectbed, random_lines1, cat1, Filter1, datamash_ops, Cut1, tp_cat, fasta_compute_length, bedtools_sortbed, addValue, tp_sort_header_tool, fasta_filter_by_lengthMapping, Read mapping, Sequence alignment
Training: 16S rRNA Analysis with Nanopore Sequencing Readshttps://usegalaxy.eu08eb5e55109c4d9chttps://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9cmetagenomics, name:microGalaxy2023-12-142023-12-1400taxonomy_krona_chart, Remove beginning1, tp_replace_in_line, multiqc, porechop, fastqc, kraken2, fastp, datamash_reverseSequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Validation, Visualisation, Statistical calculation
Main Metatranscriptomics Analysishttps://usegalaxy.eu7a08ecdf23e0c7a3https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierepname:microGalaxy2023-12-142023-12-1400MIT
Copy Of GTN Training - Antibiotic Resistance Detectionhttps://usegalaxy.eu44e53ea319e07daahttps://usegalaxy.eu/published/workflow?id=44e53ea319e07daametagenomics, name:microGalaxy2023-12-142023-12-1400bandage_image, staramr_search, gfa_to_fa, nanoplot, PlasFlow, miniasm, racon, unicycler, minimap2Aggregation, Mapping assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequence analysis, Scatter plot plotting, De-novo assembly
Identification of the micro-organisms in a beer using Nanopore sequencinghttps://usegalaxy.eu0590554db9794d13https://usegalaxy.eu/published/workflow?id=0590554db9794d13Bérénice Batut, Teresa Müller, Polina PoluninaMetagenomics, name:microGalaxy2023-12-142023-12-1400taxonomy_krona_chart, Filter1, porechop, fastqc, kraken2, fastp, krakentools_kreport2kronaAggregation, Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Statistical calculation, VisualisationMIT
workflow-generate-dataset-for-assembly-tutorialhttps://usegalaxy.euce5c16ac23c4fbb1https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1name:microGalaxy2023-12-142023-12-1400tp_cat, bowtie2, seqtk_subseq, ngsutils_bam_filter, megahit, filter_tabular, bamtools, cutadapt, random_lines1, fastqc, bg_uniqSequence composition calculation, Data handling, Variant calling, Statistical calculation, Read pre-processing, Sequence alignment analysis, Sequence file editing, Genome assembly, Formatting, Sequence contamination filtering, Primer removal, Sequencing quality control, Sequence trimming, Read mapping
Metagenomics assembly tutorial workflowhttps://usegalaxy.eu62c47e3c9d4f3aa3https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3name:microGalaxy2023-12-142023-12-1400bandage_image, bowtie2, collection_column_join, megahit, metaspades, quast, bandage_info, megahit_contig2fastgGenome assembly, Sequence assembly visualisation, Sequence assembly validation, Read mapping, Visualisation
WGS Part In "Analyses Of Metagenomics Data - The Global Picture"https://usegalaxy.euc2b7ec5aacfc6107https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107metagenomics, name:microGalaxy2023-12-142023-12-1400taxonomy_krona_chart, humann2_renorm_table, humann2, metaphlan2, humann2_regroup_table, metaphlan2kronaVisualisation
Taxonomic Profiling and Visualization of Metagenomic Datahttps://usegalaxy.eu4f0daf8e9dd54127https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127Bérénice BatutMetagenomics, name:microGalaxy2023-12-142023-12-1400taxonomy_krona_chart, __UNZIP_COLLECTION__, interactive_tool_pavian, interactive_tool_phinch, est_abundance, kraken2, metaphlan, krakentools_kreport2krona, kraken_biomPhylogenetic tree analysis, Aggregation, Nucleic acid sequence analysis, Taxonomic classification, Statistical calculation, VisualisationMIT
Amplicon Tutorialhttps://usegalaxy.eu565c989730f68362https://usegalaxy.eu/published/workflow?id=565c989730f68362metagenomics, name:microGalaxy2023-12-142023-12-1400mothur_make_group, mothur_make_biom, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_pre_cluster, krona-text, mothur_count_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_make_shared, mothur_summary_seqs, mothur_merge_filesSequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding
Microbial Variant Callinghttps://usegalaxy.eu515ef1601bc24a6chttps://usegalaxy.eu/published/workflow?id=515ef1601bc24a6cvariant-analysis, name:microGalaxy2023-12-142023-12-1400snippy, jbrowseVariant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation
Calling variants in non-diploid systemshttps://usegalaxy.eu291c36e1b18e9debhttps://usegalaxy.eu/published/workflow?id=291c36e1b18e9debvariant-analysis, name:microGalaxy2023-12-142023-12-1400freebayes, Cut1, picard_MergeSamFiles, vcf2tsv, picard_MarkDuplicates, bwa_mem, bamFilter, bamleftalign, fastqc, vcffilter2Sequence composition calculation, Generation, Data handling, Variant calling, Statistical calculation, Genome indexing, Sequence alignment, Sequence alignment analysis, Formatting, Sequencing quality control, Read mapping
Training: 16S rRNA Sequencing With Mothur: Main Tutorialhttps://usegalaxy.euc67d2e75eeb4fd19https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19metagenomics, name:microGalaxy2023-12-142023-12-1400mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_remove_groups, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_seq_error, mothur_tree_shared, mothur_cluster, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_get_groups, mothur_summary_single, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearchSequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding
Comparative gene analysishttps://usegalaxy.eu86900be4282d4b1dhttps://usegalaxy.eu/published/workflow?id=86900be4282d4b1dAnton Nekrutenkovgp, genome-annotation, name:microGalaxy2023-12-142023-12-1400Cut1, cat1, Filter1, bg_diamond, regexColumn1, rapidnj, bg_diamond_view, rbc_mafft, gops_intersect_1, tp_split_on_column, Add_a_column1, tab2fasta, collapse_dataset, join1Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis
Unicycler traininghttps://usegalaxy.eu8f3ce55d44d9f369https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369assembly, name:microGalaxy2023-12-142023-12-1400multiqc, prokka, quast, fastqc, unicyclerAggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction
Apollo Load Testhttps://usegalaxy.eu3c233cc56d4df8b0https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0genome-annotation, name:microGalaxy2023-12-142023-12-1400list_organism, create_account, create_or_update, jbrowse, iframeGenome visualisation
Genome Annotation with Prokka [Feb 2020]https://usegalaxy.eue1894c36f1ab4ab4https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4genome-annotation, name:microGalaxy2023-12-142023-12-1400prokka, jbrowseGenome annotation, Coding region prediction, Genome visualisation, Gene prediction
Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL)https://usegalaxy.eu152223c8aed27357https://usegalaxy.eu/published/workflow?id=152223c8aed27357wmdi, name:microGalaxy2023-12-142023-12-1400tp_easyjoin_tool, regex1, tp_text_file_with_recurring_lines, gff2bed1, jbrowse, tbl2gff3, tab2fasta, tp_cut_tool, join1, bandage_image, staramr_search, Grep1, circos_interval_to_tile, PlasFlow, tp_split_on_column, bg_column_arrange_by_header, minimap2, medaka_consensus_pipeline, Filter1, tp_head_tool, trimmomatic, circos_wiggle_to_scatter, ncbi_blastn_wrapper, circos, Add_a_column1, flye, fasta2tab, fasta_compute_length, tp_cat, Cut1, circos_gc_skew, nanoplot, prokka, deeptools_bam_coverage, regex_replace, tp_sort_header_toolSequence analysis, Variant calling, Mapping assembly, Sequence assembly, Gene prediction, Sequence visualisation, Cross-assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Genome visualisation, Coding region prediction, Genome annotation, Base-calling, Scatter plot plotting, De-novo assembly
Mtb phylogenyhttps://usegalaxy.eu875b3ca170ac12a1https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1evolution, name:microGalaxy2023-12-142023-12-1400raxml, interactive_tool_rstudioPhylogenetic tree analysis, Sequence analysis
From VCFs to SNP distance matrixhttps://usegalaxy.eu6d333ed886aab471https://usegalaxy.eu/published/workflow?id=6d333ed886aab471evolution, name:microGalaxy2023-12-142023-12-1400tp_cat, tb_variant_filter, bcftools_consensus, snp_dists, snp_sites
From Fastqs to VCFs and BAMshttps://usegalaxy.eu3a8fde248a4d0383https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383evolution, name:microGalaxy2023-12-142023-12-1400__MERGE_COLLECTION__, tb_variant_filter, trimmomatic, snippyVariant calling, Phylogenetic tree visualisation, Phylogenetic tree generation
From BAMs to drug resistance prediction with TB-profilerhttps://usegalaxy.eud0d6dae0d1eecc21https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21evolution, name:microGalaxy2023-12-142023-12-1400tb_profiler_profile, tp_cat, addName, tp_sed_tool, tp_replace_in_line, samtools_view, tp_grep_tool, __MERGE_COLLECTION__Antimicrobial resistance prediction
M. tuberculosis Variant Analysis tutorialhttps://usegalaxy.eu3ff4dbcc7a602e6bhttps://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6bPeter van Heusdenvariant-analysis, prokaryote, name:microGalaxy2023-12-142023-12-1400tb_profiler_profile, tb_variant_filter, trimmomatic, multiqc, jbrowse, tbvcfreport, snippy, fastqc, kraken2Sequence composition calculation, Phylogenetic tree generation, Variant calling, Validation, Phylogenetic tree visualisation, Statistical calculation, Antimicrobial resistance prediction, Sequencing quality control, Genome visualisation, Taxonomic classificationMIT
Compute Allel Frequency Table from paired readshttps://usegalaxy.eu21a39ac4c1becb31https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31name:microGalaxy, HPylori2023-12-132023-12-1322freebayes, tp_awk_tool, bowtie2, vcf2tsv, snpSift_filter, bcftools_norm, bcftools_viewVariant calling, Statistical calculation, Read mapping
Reference genome choice (indels, coverage, depth) for short readshttps://usegalaxy.eu61fe08fb3d5e83f8https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8name:microGalaxy, HPylori2023-10-272023-12-131313freebayes, tp_cat, bowtie2, vcf2tsv, collection_element_identifiers, samtools_coverage, collapse_dataset, bcftools_norm, samtools_depthVariant calling, Statistical calculation, Read mapping
MGnify amplicon rRNA-prediction + ITShttps://usegalaxy.eu437704898229dfb6https://usegalaxy.eu/published/workflow?id=437704898229dfb6MGnify_Amplicon_Showcase, name:microGalaxy2023-12-122023-12-1311taxonomy_krona_chart, tp_awk_tool, query_tabular, cmsearch_deoverlap, gops_concat_1, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseq, bedtools_maskfastabedFormatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, Visualisation
MGnify amplicon QChttps://usegalaxy.eu8f415b0c409f56f7https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7MGnify_Amplicon_Showcase, name:microGalaxy2023-12-132023-12-1311__UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, iuc_pear, prinseq, fastqc, tp_find_and_replace, fastp, fastq_dumpSequence composition calculation, Data handling, Validation, Sequence merging, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Sequence trimming
Cloud-Aerosole MT-MG Functional Profilinghttps://usegalaxy.eu4566262dd0acc8abhttps://usegalaxy.eu/published/workflow?id=4566262dd0acc8abmetagenomics, metatranscriptomics, name:microGalaxy2021-11-102023-12-0722featurecounts, bowtie2, multiqcValidation, Sequencing quality control, Read summarisation, Read mapping, RNA-Seq quantification
Cloud-Aerosole MT-MG Reference Gene Catalog Buildinghttps://usegalaxy.eu9b9e1e28f3683f92https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92metagenomics, metatranscriptomics, name:microGalaxy2021-11-012023-12-077272dbbuilder, translate_nucleotides, bowtie2, cat1, bg_diamond, cd_hit, kofamscan, metagene_annotator, bg_diamond_makedb, multiqc, megahit, bedtools_getfastabed, quast, fastqc, metaeuk_easy_predict, eggnog_mapperSequence clustering, Information extraction, Query and retrieval, Homology-based gene prediction, Visualisation, Genome assembly, Sequencing quality control, Genome annotation, Mapping, Sequence analysis, Sequence composition calculation, Sequence assembly validation, Sequence annotation, Validation, Statistical calculation, Fold recognition, Gene functional annotation, Sequence alignment analysis, Read mapping
Cloud-Aerosole MT-MG Pre-Processinghttps://usegalaxy.eubb604ff5e010e7abhttps://usegalaxy.eu/published/workflow?id=bb604ff5e010e7abmetagenomics, metatranscriptomics, name:microGalaxy2021-11-012023-12-075151trimmomatic, multiqc, fastqcSequence composition calculation, Sequencing quality control, Validation, Statistical calculation
Cloud Aerosol MT-MG Contamination Filteringhttps://usegalaxy.eubdc7cfaac0db2eabhttps://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eabmetagenomics, metatranscriptomics, name:microGalaxy2022-06-292023-12-072828recentrifuge, bowtie2, seq_filter_by_id, filter_tabular, kraken2, fastq_to_tabularTaxonomic classification, Expression analysis, Read mapping, Cross-assembly
Cloud-Aerosole MT-MG Taxonomic Profilinghttps://usegalaxy.eue69b555faa6bb962https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962metagenomics, metatranscriptomics, name:microGalaxy2022-09-032023-12-071818recentrifuge, interactive_tool_phinch, kraken2, maaslin2, kraken_biomFiltering, Standardisation and normalisation, Taxonomic classification, Statistical calculation, Expression analysis, Visualisation, Cross-assembly
Main Metatranscriptomics Analysis 24.08.2023https://usegalaxy.eu81033ff723b9f22dhttps://usegalaxy.eu/published/workflow?id=81033ff723b9f22dmicrobiome2023-08-242023-11-0766
pAllori ASiam Functional Information MThttps://usegalaxy.eua7a6d8ecc2795f58https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasrname:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:functionalProfiling2023-07-072023-07-0733Cut1, humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, tp_find_and_replace, humann_rename_tableSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMIT
pAllori ASiam Community Profile MThttps://usegalaxy.eu05f5f040337786bfhttps://usegalaxy.eu/published/workflow?id=05f5f040337786bfEngy Nasr, Bérénice Batutname:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:communityProfiling2023-06-302023-07-0633Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlanPhylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editingMIT
pAllori ASiam Preprocessing MThttps://usegalaxy.eu72e3e5fdc766e24ahttps://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24aBérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasrname:microGalaxy, name:AdaptedASiam, name:metatranscriptomics, name:preprocessing2023-06-302023-07-0622__FLATTEN__, multiqc, bg_sortmerna, fastq_paired_end_interlacer, cutadapt, fastqcSequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimmingMIT
Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identificationhttps://usegalaxy.eu3f0b104a74acf869https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869Engy Nasr, Bérénice Batutmicrobiome, nanopore2023-01-162023-05-3088clair3, bcftools_consensus, bcftools_norm, snpSift_filter, minimap2, snpSift_extractFieldsVariant calling, Pairwise sequence alignmentMIT
Pathogen-Detection-Nanopore-Gene-based-pathogenic-Identificationhttps://usegalaxy.eu2b888e200dfd91bchttps://usegalaxy.eu/published/workflow?id=2b888e200dfd91bcEngy Nasr, Bérénice Batutmicrobiome, nanopore2023-01-102023-05-302020mlst, bandage_image, Cut1, medaka_consensus_pipeline, cat1, add_line_to_file, abricate, tab2fasta, compose_text_param, tp_find_and_replace, tp_replace_in_column, flye, fasta2tabMapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assemblyMIT
Pathogen Detection-Nanopore-Taxonomy-Profiling-and-Visualizationhttps://usegalaxy.eua0ea6fc756dd17eahttps://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17eaEngy Nasr, Bérénice Batutmicrobiome, nanopore2023-02-022023-05-3044kraken2, interactive_tool_phinch, kraken_biomTaxonomic classificationMIT
Pathogen-Detection-Nanopore-Taxonomy-Profiling-and-Visualization-with-kronahttps://usegalaxy.eued2df13cfbc86b99https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99Engy Nasr, Bérénice Batutmicrobiome, nanopore2023-02-172023-05-3066kraken2, krakentools_kreport2krona, krona-textTaxonomic classification, Aggregation, VisualisationMIT
Pathogen-Detection-Nanopore-Pre-Processinghttps://usegalaxy.eu889f2782ad82bd69https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69Bérénice Batut, Engy Nasrmicrobiome, nanopore2023-02-022023-05-3066porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastpSequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plottingMIT
Resistome workflow Pig Nov2021 (imported from uploaded file)https://usegalaxy.eu25850714d13f0b0fhttps://usegalaxy.eu/published/workflow?id=25850714d13f0b0fMetagenomics, Resistome2023-05-222023-05-2300bowtie2, resistome_analyzer, samtools_sort, bam_to_sam, rarefaction_analyzer, snpfinder, XY_Plot_1, fastpSequencing quality control, Sequence contamination filtering, Read mapping
ASaiM-MT:metaphlanhttps://usegalaxy.eued0ad728cf21702bhttps://usegalaxy.eu/published/workflow?id=ed0ad728cf21702bASaiM2023-05-172023-05-1733taxonomy_krona_chart, metaphlan2, graphlan, format_metaphlan2_output, export2graphlan, graphlan_annotate, fastq_paired_end_interlacer, metaphlan2kronaPhylogenetic inference, Phylogenetic tree visualisation, Visualisation, Formatting, Conversion, Taxonomic classification, Phylogenetic tree editing
Training: 16S rRNA RNIMUhttps://usegalaxy.eudadca1020f586338https://usegalaxy.eu/published/workflow?id=dadca1020f586338metagenomics2023-04-242023-04-2788mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_tree_shared, mothur_chimera_vsearch, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, newick_display, mothur_count_groups, mothur_make_shared, mothur_rarefaction_singleSequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding
MetaPhttps://usegalaxy.eu96d198ed953449fdhttps://usegalaxy.eu/published/workflow?id=96d198ed953449fdname:microgalaxy2020-01-302023-03-1622maxquantHeat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering
MetaG_extendedhttps://usegalaxy.eu6158c3b5fc12044ehttps://usegalaxy.eu/published/workflow?id=6158c3b5fc12044ename:microgalaxy2023-02-102023-03-162222coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wfData retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction
Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.1)https://usegalaxy.eub77e3b08092fa73ehttps://usegalaxy.eu/published/workflow?id=b77e3b08092fa73eViktoria Isabel Schwarz, Wolfgang Maierpox, virology2023-03-022023-03-0211ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignmentMIT
MetaThttps://usegalaxy.eu385cc7df70d7916bhttps://usegalaxy.eu/published/workflow?id=385cc7df70d7916bname:microgalaxy2020-01-272023-02-271616kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqcSequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling
Nanopore Datasets - Pre-Processinghttps://usegalaxy.eu57d3109f32defa3bhttps://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, , Bérénice Batut, , Engy Nasrmicrobiome, nanopore2022-08-072023-01-297171porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastpSequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plottingMIT
Bacterial genome assembly - IZSPBhttps://usegalaxy.eu37da7b42cb063a3ahttps://usegalaxy.eu/published/workflow?id=37da7b42cb063a3aassembly, bacterial, genome2021-07-272022-12-031818mlst, spades, abricate, multiqc, prokka, quast, abricate_summary, fastpSequence assembly validation, Validation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Multilocus sequence typing, Sequence contamination filtering, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction
16S rDNA microbial analisys + MUSCLE mothurhttps://usegalaxy.eu6d06bd22f206e176https://usegalaxy.eu/published/workflow?id=6d06bd22f206e17616S, mothur, microbial, microbiome, OTU, Cluster, Rarefaction2021-08-092022-07-2988mothur_chimera_uchime, mothur_get_oturep, mothur_unique_seqs, mothur_rarefaction_single, mothur_dist_seqs, mothur_remove_seqs, muscle, mothur_clusterSequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding
Metatranscriptomics-WF3: Functional Information (quick)https://usegalaxy.eu5ce8a472e6e95c60https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60metagenomics2021-05-252021-11-0988humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_tableSpecies frequency estimation, Taxonomic classification, Phylogenetic analysis
Metatranscriptomics-WF3: Functional Informationhttps://usegalaxy.eu23dd2253da51e22ehttps://usegalaxy.eu/published/workflow?id=23dd2253da51e22emetagenomics2021-05-252021-11-0966humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_tableSpecies frequency estimation, Taxonomic classification, Phylogenetic analysis
Metatranscriptomics - analyze human RNA-seq data with Kraken (imported from uploaded file)https://usegalaxy.euee0005a5487653bahttps://usegalaxy.eu/published/workflow?id=ee0005a5487653bametatranscriptomics, Kraken, RNA-seq, microbiome2021-10-182021-10-1822taxonomy_krona_chart, Kraken2Tax, picard_SamToFastq, trimmomatic, samtools_view, bwa, fastqc, kraken2Sequence composition calculation, Generation, Statistical calculation, Genome indexing, Sequence alignment, Visualisation, Formatting, Sequencing quality control, Taxonomic classification, Read mapping
Taxonomic and functional community profiling of raw metagenomic shotgun data workflowhttps://usegalaxy.eua8f829deb69b30abhttps://usegalaxy.eu/published/workflow?id=a8f829deb69b30abasaim2021-06-222021-06-241414taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann_unpack_pathways, Grep1, format_metaphlan2_output, graphlan_annotate, combine_metaphlan2_humann2, humann, bg_sortmerna, export2graphlan, humann_regroup_table, fastqc, Cut1, humann2_genefamilies_genus_level, graphlan, multiqc, humann_renorm_table, metaphlan, humann_rename_tableSequence similarity search, Phylogenetic analysis, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Nucleic acid sequence analysis, Species frequency estimation, Sequence comparison
Metatranscriptomcis-WF2: Community Profilehttps://usegalaxy.eu19de5cbae7f48103https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103metagenomics2021-05-252021-05-2522Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlanPhylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editing
Metatranscriptomics-WF1: Preprocessinghttps://usegalaxy.euf6e8a63283262518https://usegalaxy.eu/published/workflow?id=f6e8a63283262518metagenomics2021-05-252021-05-2522bg_sortmerna, multiqc, fastq_paired_end_interlacer, cutadapt, fastqcSequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming
ASaiM-MThttps://usegalaxy.eudfc2c53ac3103effhttps://usegalaxy.eu/published/workflow?id=dfc2c53ac3103effASaiM2020-12-042020-12-0411taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann2, Grep1, format_metaphlan2_output, graphlan_annotate, Grouping1, humann2_unpack_pathways, metaphlan2krona, metaphlan2, combine_metaphlan2_humann2, bg_sortmerna, export2graphlan, fastqc, humann2_renorm_table, humann2_genefamilies_genus_level, graphlan, multiqc, tp_sort_header_toolSequence similarity search, Phylogenetic tree visualisation, Visualisation, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Sequence comparison
Workflow 3: Functional Information [Metatranscriptomics]https://usegalaxy.euc817aefc77933d79https://usegalaxy.eu/published/workflow?id=c817aefc77933d79metagenomics2020-07-132020-07-1411humann2_renorm_table, humann2, humann2_unpack_pathways, group_humann2_uniref_abundances_to_go
0_Short-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020)https://usegalaxy.eu374797e58377c40fhttps://usegalaxy.eu/published/workflow?id=374797e58377c40fAssembly, Unicycler, StarAMR, Bacterial, Prokka, Short-Read, Illumina2020-06-242020-06-2444bandage_image, staramr_search, multiqc, prokka, quast, bandage_info, fastqc, unicycler, fastpAggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequence contamination filtering, Sequencing quality control, Sequence assembly visualisation, Coding region prediction, Genome annotation, Gene prediction
0_Hybrid_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020)https://usegalaxy.euecf48fa50af560a0https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0Hybrid, Assembly, ONT, Unicycler, StarAMR, Bacterial, Prokka2020-06-242020-06-241313filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, multiqc, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, fastqc, unicycler, fastp, minimap2Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Pairwise sequence alignment, Scatter plot plotting, Gene prediction
0_Long-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020)https://usegalaxy.euea485dbabc76488dhttps://usegalaxy.eu/published/workflow?id=ea485dbabc76488dAssembly, ONT, Unicycler, StarAMR, Bacterial, Prokka, Coverage2020-06-242020-06-2433filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, unicycler, minimap2Aggregation, Sequence assembly validation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Scatter plot plotting, Gene prediction
MetaGalaxyhttps://usegalaxy.eu5826e573b6f93762https://usegalaxy.eu/published/workflow?id=5826e573b6f93762Long_Read, Metagenomics, Assembly, AMR, Taxonomy, Gene_Annotation, Long_Read2020-01-222020-04-2111Cut1, filtlong, bandage_image, mlst, abricate, nanoplot, Krona, racon, prokka, jbrowse, quast, bandage_info, kraken2, meta_flye, minimap2Sequence assembly validation, Mapping assembly, Visualisation, Taxonomic classification, Filtering, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Genome visualisation, Pairwise sequence alignment, Scatter plot plotting, Gene prediction
MetaGalaxy (4x polishing w Racon)https://usegalaxy.eua337bfb2eb1e583fhttps://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583fNanopore, Metagenomics, ONT2020-01-312020-02-1044Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flyeMapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction
MetaGalaxyhttps://usegalaxy.eua84bac86ec183d46https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46Nanopore, Metagenomics, ONT2020-01-242020-02-1088Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flyeMapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction
16S microbial analysis (Mothur)https://usegalaxy.euce21961260fe4351https://usegalaxy.eu/published/workflow?id=ce21961260fe4351Metagenomics, Mothur, 16S2018-09-222018-09-2211mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_heatmap_bin, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, collapse_dataset, mothur_make_contigs, mothur_pcoa, mothur_classify_otu, mothur_get_oturep, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, fasttree, mothur_venn, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearchSequence clustering, Phylogenetic analysis, Phylogenetic tree generation (from molecular sequences), Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding, Phylogenetic tree generation (maximum likelihood and Bayesian methods)
ASaiM - Metagenomic assembly with MetaSPAdeshttps://usegalaxy.eu579ff83177c5ee09https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09ASaiM2018-01-172018-08-0333bowtie2, valet, multiqc, metaspades, quast, trim_galore, fastqcSequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping
ASaiM - Metagenomic assembly with MEGAHIThttps://usegalaxy.eu1524b189069b42a5https://usegalaxy.eu/published/workflow?id=1524b189069b42a5ASaiM2018-01-172018-08-0344bowtie2, valet, multiqc, megahit, quast, trim_galore, fastqcSequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping
ASaiM - Shotgun workflow for paired-end data collectionhttps://usegalaxy.eu329cf724a21f13echttps://usegalaxy.eu/published/workflow?id=329cf724a21f13ecASaiM2018-04-302018-04-3011
Shotgun workflow for paired-end data (imported from uploaded file)https://usegalaxy.eu358db17bfc1ee330https://usegalaxy.eu/published/workflow?id=358db17bfc1ee330ASaiM2018-01-292018-04-3000fastq_join
ASaiM - Shotgun workflow for single-end data collectionhttps://usegalaxy.eu1c3adfc77a138ef6https://usegalaxy.eu/published/workflow?id=1c3adfc77a138ef6ASaiM2018-01-292018-04-3022
QIIME - Illumina Overview tutorial (imported from uploaded file)https://usegalaxy.eu3acfb87be6db2303https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303ASaiM2018-01-172018-01-1700qiime_pick_open_reference_otus, qiime_split_libraries_fastq, qiime_core_diversity, qiime_validate_mapping_file, qiime_count_seqsPhylogenetic analysis, Visualisation, Sequencing quality control, Taxonomic classification, Demultiplexing
EBI Metagenomics workflow (3.0) (imported from uploaded file)https://usegalaxy.eu58955868b504c60dhttps://usegalaxy.eu/published/workflow?id=58955868b504c60dASaiM2018-01-172018-01-1700hmmer_hmmsearch, cshl_fastq_to_fasta, tp_awk_tool, tp_cat, fraggenescan, trimmomatic, seq_filter_by_id, hmmer_hmmbuild, interproscan, qiime_pick_closed_reference_otusData retrieval, Phylogenetic analysis, Sequence generation, Visualisation, Protein feature detection, Conversion, Sequencing quality control, Format validation, Database search, Taxonomic classification, Sequence motif recognition, Multiple sequence alignment, Demultiplexing, Statistical calculation, Sequence database search, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene prediction
+ +
\ No newline at end of file diff --git a/communities/microgalaxy/resources/workflows.tsv b/communities/microgalaxy/resources/workflows.tsv new file mode 100644 index 00000000..54a42a78 --- /dev/null +++ b/communities/microgalaxy/resources/workflows.tsv @@ -0,0 +1,144 @@ +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI +bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=5 Abromics None, Pierre Marin, Clea Siguret ABRomics, Assembly, FASTQ, Genomics, bacterial-genomics, paired-end, quality 2024-10-07 2024-10-07 5 5 7.0 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=6 ABRomics None, Pierre Marin, Clea Siguret ABRomics, FASTQ, Genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2024-10-12 2024-10-12 6 6 6.0 recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu f21d6a40a10a8ae8 https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8 microbiome 2024-09-30 2024-10-01 1 1 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_remove_groups, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_seq_error, mothur_tree_shared, mothur_cluster, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_get_groups, mothur_summary_single, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearch Sequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding +MGnify amplicon summary tables https://usegalaxy.eu 05dc8f4321a42cdc https://usegalaxy.eu/published/workflow?id=05dc8f4321a42cdc Rand Zoabi MGnify_Amplicon, amplicon, metagenomics 2024-05-22 2024-09-27 68 68 tp_awk_tool, query_tabular, collection_column_join, Grouping1, filter_tabular MIT +virannot_post_CLC https://usegalaxy.eu 86465932556bc96c https://usegalaxy.eu/published/workflow?id=86465932556bc96c Marie Lefebvre virology, otu, virannot, RPS, virus 2024-08-21 2024-09-26 6 6 taxonomy_krona_chart, virannot_blast2tsv, ncbi_tblastx_wrapper, virAnnot_rps2tsv, krona-text, ncbi_rpstblastn_wrapper, virannot_otu Sequence clustering, Sequence cluster visualisation, Sequence annotation, Visualisation +bacterial_genome_annotation (release v1.1.4) https://usegalaxy.eu d8db0b2e30370b84 https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-26 2024-09-26 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.1.2) https://usegalaxy.eu 723e718f37e9ab91 https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91 abromics-consortium, ABRomics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-26 2024-09-26 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +amr_gene_detection (release v1.1.2) https://usegalaxy.eu e37cc0b64774561b https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-26 2024-09-26 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Taxonomic classification, Aggregation, Visualisation MIT +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, name:IWC 2024-09-19 2024-09-19 1 1 Cut1, samtools_fastx, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, Grep1, collection_column_join, multiqc, porechop, nanoplot, Add_a_column1, fastqc, kraken2, fastp, collapse_dataset, minimap2, bamtools_split_mapped Aggregation, Sequence composition calculation, Data handling, Validation, Statistical calculation, Visualisation, Sequence alignment analysis, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Taxonomic classification, Scatter plot plotting MIT +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.eu 77e5bbd317750915 https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:PathoGFAIR, name:IWC, name:microGalaxy 2024-09-19 2024-09-19 1 1 param_value_from_file, bandage_image, medaka_consensus_pipeline, collection_element_identifiers, abricate, split_file_to_collection, tab2fasta, compose_text_param, tp_find_and_replace, __BUILD_LIST__, flye, fasta2tab Mapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assembly MIT +Allele-based Pathogen Identification (release v0.1) https://usegalaxy.eu d215a2e554fd83bc https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depth Variant calling, Pairwise sequence alignment MIT +Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.eu cdf2f02428f5f83f https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-09-19 2024-09-19 1 1 Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depth Variant calling, Pairwise sequence alignment MIT +bacterial_genome_annotation (release v1.0) https://usegalaxy.eu 61948fcaefa1418a https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-19 2024-09-19 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +bacterial_genome_annotation (release v1.1) https://usegalaxy.eu 8792eaecb69fbc26 https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-19 2024-09-19 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +bacterial_genome_annotation (release v1.1.1) https://usegalaxy.eu 36ea584e0f60893e https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-19 2024-09-19 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +bacterial_genome_annotation (release v1.1.2) https://usegalaxy.eu bcd50e655809cfcb https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-19 2024-09-19 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +bacterial_genome_annotation (release v1.1.3) https://usegalaxy.eu 4a218fb93d78ba67 https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fasta, ABRomics, bacterial-genomics, Annotation, genome-annotation 2024-09-19 2024-09-19 1 1 integron_finder, plasmidfinder, bakta, tooldistillator_summarize, tooldistillator, isescan Parsing, Nucleic acid feature detection, Structural variation detection, Data handling, Genome assembly, Protein feature detection, Multilocus sequence typing, Scaffolding, Genome annotation, Sequence motif recognition GPL-3.0-or-later +Quality and Contamination Control For Genome Assembly (release v1.0) https://usegalaxy.eu 884a4415b669690c https://usegalaxy.eu/published/workflow?id=884a4415b669690c ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming 2024-09-19 2024-09-19 1 1 recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Quality and Contamination Control For Genome Assembly (release v1.1) https://usegalaxy.eu aafcfcb585c5ca75 https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming 2024-09-19 2024-09-19 1 1 recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Quality and Contamination Control For Genome Assembly (release v1.1.1) https://usegalaxy.eu 0c47571d20535426 https://usegalaxy.eu/published/workflow?id=0c47571d20535426 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming 2024-09-19 2024-09-19 1 1 recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Quality and Contamination Control For Genome Assembly (release v1.1.2) https://usegalaxy.eu 0a82eb8b44d9d502 https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret Genomics, fastq, bacterial-genomics, taxonomy-assignment, paired-end, quality, ABRomics, trimming 2024-09-19 2024-09-19 1 1 recentrifuge, est_abundance, tooldistillator_summarize, kraken2, fastp, tooldistillator Parsing, Data handling, Statistical calculation, Expression analysis, Cross-assembly, Sequence contamination filtering, Sequencing quality control, Taxonomic classification GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.0) https://usegalaxy.eu 3d937648809ca4e7 https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7 abromics-consortium, Abromics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.1) https://usegalaxy.eu fca458178b3c794a https://usegalaxy.eu/published/workflow?id=fca458178b3c794a abromics-consortium, ABRomics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +Bacterial Genome Assembly using Shov (release v1.1.1) https://usegalaxy.eu 4216424f032c055f https://usegalaxy.eu/published/workflow?id=4216424f032c055f abromics-consortium, ABRomics, Pierre Marin, Clea Siguret fastq, Genomics, bacterial-genomics, paired-end, assembly, quality, ABRomics 2024-09-19 2024-09-19 1 1 refseq_masher_matches, bandage_image, tooldistillator_summarize, quast, bandage_info, shovill, tooldistillator Genome assembly, Parsing, Sequence assembly visualisation, Sequence assembly validation, Data handling, Visualisation GPL-3.0-or-later +amr_gene_detection (release v1.0) https://usegalaxy.eu 41d207d06a32ba05 https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +amr_gene_detection (release v1.1) https://usegalaxy.eu abe85758e77c78e6 https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6 ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +amr_gene_detection (release v1.1.1) https://usegalaxy.eu f30f8e7dcd50cd0d https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d ABRomics, abromics-consortium, Pierre Marin, Clea Siguret fasta, Genomics, ABRomics, antibiotic-resistance, antimicrobial-resistance-genes, antimicrobialresistance, bacterial-genomics, AMR, AMR-detection 2024-09-19 2024-09-19 1 1 amrfinderplus, staramr_search, abricate, tooldistillator_summarize, tooldistillator Parsing, Antimicrobial resistance prediction, Data handling GPL-3.0-or-later +dada2 amplicon analysis pipeline - for paired en (release v0.2) https://usegalaxy.eu 642f4c47028031d7 https://usegalaxy.eu/published/workflow?id=642f4c47028031d7 Matthias Bernt, UFZ Leipzig name:amplicon 2024-09-19 2024-09-19 1 1 dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCounts Variant calling, DNA barcoding MIT +Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.2) https://usegalaxy.eu 6e1fe7372e93fae0 https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0 Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2024-09-19 2024-09-19 1 1 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +LŠMB: Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 181e751be8dd9abc https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc Bérénice Batut, Teresa Müller, Polina Polunina Microbiome 2024-09-08 2024-09-08 0 0 taxonomy_krona_chart, Filter1, porechop, nanoplot, fastqc, kraken2, fastp, krakentools_kreport2krona Aggregation, Sequence composition calculation, Statistical calculation, Visualisation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +MGnify's amplicon pipeline v5.0 - Quality control SE https://usegalaxy.eu b7166aff73e5d81c https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c MGnify - EMBL, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-03-25 2024-08-21 13 13 trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, prinseq, fastqc, tp_find_and_replace, fastq_filter Sequence composition calculation, Sequence trimming, Sequence contamination filtering, Sequencing quality control, Statistical calculation, Validation, Read pre-processing Apache-2.0 +MGnify's amplicon pipeline v5.0 - ITS https://usegalaxy.eu 169327ba670607d1 https://usegalaxy.eu/published/workflow?id=169327ba670607d1 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-05-06 2024-08-21 23 23 __FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, __FILTER_EMPTY_DATASETS__, collection_element_identifiers, biom_convert, mapseq, bedtools_maskfastabed Mapping, Formatting, Visualisation, k-mer counting Apache-2.0 +MGnify's amplicon pipeline v5.0 - Quality control PE https://usegalaxy.eu f9648091c06171cd https://usegalaxy.eu/published/workflow?id=f9648091c06171cd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, amplicon, metagenomics 2024-05-27 2024-08-21 14 14 __UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, fastq_filter, prinseq, mgnify_seqprep, fastqc, tp_find_and_replace, fastp Sequence composition calculation, Validation, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence trimming Apache-2.0 +MGnify's amplicon pipeline v5.0 - rRNA prediction https://usegalaxy.eu 0c3eee883f5ab977 https://usegalaxy.eu/published/workflow?id=0c3eee883f5ab977 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, metagenomics, amplicon 2024-05-06 2024-08-21 29 29 __FILTER_FROM_FILE__, taxonomy_krona_chart, tp_awk_tool, query_tabular, __FILTER_EMPTY_DATASETS__, cmsearch_deoverlap, collection_element_identifiers, gops_concat_1, cshl_fasta_formatter, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseq Formatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, Visualisation Apache-2.0 +MGnify's amplicon pipeline v5.0 - complete https://usegalaxy.eu 02f90a96d01fed4f https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep MGnify_Amplicon, metagenomics, amplicon 2024-05-06 2024-08-21 79 79 fasterq_dump, __MERGE_COLLECTION__ Data handling Apache-2.0 +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microGalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-08-13 69 69 lotus2, taxonomy_krona_chart, ampvis2_load, __FLATTEN__, trimmomatic, collection_column_join, multiqc, ampvis2_ordinate, cutadapt, unzip, fastqc, kraken2, tp_cut_tool, krakentools_kreport2krona, ampvis2_heatmap Aggregation, Sequence composition calculation, Sequence trimming, Sequence feature detection, Validation, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Analysis, Sequencing quality control, Taxonomic classification, DNA barcoding MIT +Capripox isolate subtyping and consensus genome generation from WGS data https://usegalaxy.eu 629e57958afed44c https://usegalaxy.eu/published/workflow?id=629e57958afed44c Wolfgang Maier CaPV, VETLAB, virology 2024-07-28 2024-08-02 9 9 param_value_from_file, fasta_regex_finder, __FLATTEN__, qualimap_bamqc, ivar_consensus, __FILTER_FAILED_DATASETS__, bwa_mem, Show beginning1, read_it_and_keep, samtools_view, multiqc, tp_find_and_replace, fastp, collapse_dataset, __EXTRACT_DATASET__, vapor Generation, Data retrieval, Validation, Genome indexing, Sequence alignment, Filtering, Genome alignment, Sequence contamination filtering, Sequencing quality control, De-novo assembly, Read mapping AGPL-3.0-or-later +Pox Virus Illumina Amplicon Workflow from half-genomes https://usegalaxy.eu a31100610fba17a1 https://usegalaxy.eu/published/workflow?id=a31100610fba17a1 Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2024-08-02 2024-08-02 0 0 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microGalaxy, name:pallori, name:BloodRNA, name:UMI, name:Barcode, name:transcriptomics 2023-07-02 2024-07-29 37 37 umi_tools_extract, __FLATTEN__, featurecounts, __FILTER_FAILED_DATASETS__, collection_column_join, multiqc, fastqc, rna_star Validation, Sequence composition calculation, Statistical calculation, Sequencing quality control, Read summarisation, Sequence alignment, RNA-Seq quantification MIT +pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microGalaxy, name:WGS 2024-07-16 2024-07-28 16 16 freebayes, Remove beginning1, ggplot2_heatmap, bowtie2, __FLATTEN__, vcf2tsv, tp_awk_tool, regexColumn1, abricate, trimmomatic, collection_column_join, multiqc, Grouping1, fastqc, snpSift_filter, shovill, bcftools_norm, bcftools_view Sequence composition calculation, Variant calling, Validation, Statistical calculation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Sequencing quality control, Read mapping MIT +Influenza sequence data analysis https://usegalaxy.eu bc5ced57e711acf9 https://usegalaxy.eu/published/workflow?id=bc5ced57e711acf9 Wolfgang Maier, Viktoria Isabel Schwarz AIV, VETLAB, virology 2024-07-26 2024-07-28 21 21 map_param_value, iqtree, qualimap_bamqc, seqtk_subseq, bwa_mem, Show beginning1, __RELABEL_FROM_FILE__, snipit, collapse_dataset, Grep1, tp_find_and_replace, rbc_mafft, __EXTRACT_DATASET__, vapor, __APPLY_RULES__, ivar_consensus, __UNZIP_COLLECTION__, bamtools_split_ref, Paste1, __DUPLICATE_FILE_TO_COLLECTION__, pick_value, fastp, param_value_from_file, collection_element_identifiers, samtools_view, wc_gnu Generation, De-novo assembly, Data retrieval, Data handling, Phylogenetic analysis, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence file editing, Sequence contamination filtering, Sequencing quality control, Base position variability plotting, Sequence analysis, Read mapping, Multiple sequence alignment AGPL-3.0-or-later +MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microGalaxy 2023-11-15 2024-07-11 14 14 Fasta_to_Contig2Bin, samtools_sort, metabat2_jgi_summarize_bam_contig_depths, megahit, fastq_paired_end_interlacer, semibin, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_coverage_table, coverm_genome, bowtie2, __UNZIP_COLLECTION__, das_tool, metabat2, quast, checkm_lineage_wf, concoct_merge_cut_up_clustering, concoct, drep_dereplicate, maxbin2 Sequence clustering, Sequence composition calculation, Read binning, Sequence assembly validation, Sequence assembly, Statistical calculation, Validation, Visualisation, Genome comparison, Genome assembly, Local alignment, Sequencing quality control, Genome annotation, Read mapping +PathoGFAIR https://usegalaxy.eu 0dce37adb369492c https://usegalaxy.eu/published/workflow?id=0dce37adb369492c Engy Nasr, Bérénice Batut, Paul Zierep name:microGalaxy, name:IWC, name:PathoGFAIR, name:Nanopore, name:Collection 2024-05-31 2024-07-03 93 93 MIT +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2024-04-03 2024-06-24 58 58 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2023-04-12 2024-06-24 72 72 Cut1, Remove beginning1, table_compute, clair3, tp_head_tool, bcftools_consensus, CONVERTER_gz_to_uncompressed, snpSift_extractFields, regexColumn1, Paste1, bcftools_norm, samtools_coverage, Count1, snpSift_filter, tp_cut_tool, collapse_dataset, minimap2, samtools_depth Variant calling, Pairwise sequence alignment MIT +Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:Nanopore, name:IWC 2023-04-12 2024-06-24 190 190 Cut1, samtools_fastx, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, Grep1, collection_column_join, multiqc, porechop, nanoplot, Add_a_column1, fastqc, kraken2, fastp, collapse_dataset, minimap2, bamtools_split_mapped Aggregation, Sequence composition calculation, Data handling, Validation, Statistical calculation, Visualisation, Sequence alignment analysis, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Taxonomic classification, Scatter plot plotting MIT +Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microGalaxy, name:GTN 2023-04-12 2024-06-19 8 8 kraken2, interactive_tool_phinch, kraken_biom Taxonomic classification MIT +metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microGalaxy 2023-12-14 2024-06-19 0 0 Cut1, Remove beginning1, flashlfq, regex1, query_tabular, Filter1, msconvert, tp_replace_in_line, tp_replace_in_column, search_gui, peptide_shaker, unipept Filtering, Prediction and recognition, Label-free quantification, Formatting, Visualisation +QIIME2 I: Demultiplexing (single-end) https://usegalaxy.eu 86b31ac8a7720e41 https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41 Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ name:amplicon, name:16S, name:tutorial 2024-06-12 2024-06-18 1 1 qiime2_core__tools__import, qiime2__demux__summarize, qiime2__demux__emp_single MIT +QIIME2 II: Denoising (sequence quality control) and feature table creation (single-end) https://usegalaxy.eu da17a4d690eb0ff3 https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3 Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ name:amplicon, name:16S, name:tutorial 2024-06-12 2024-06-18 1 1 qiime2__feature_table__tabulate_seqs, qiime2__feature_table__summarize, qiime2__metadata__tabulate, qiime2__dada2__denoise_single MIT +Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:PathoGFAIR, name:IWC, name:microGalaxy 2023-04-13 2024-06-05 142 142 param_value_from_file, bandage_image, medaka_consensus_pipeline, collection_element_identifiers, abricate, split_file_to_collection, tab2fasta, compose_text_param, tp_find_and_replace, __BUILD_LIST__, flye, fasta2tab Mapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assembly MIT +Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:Collection, name:microGalaxy, name:PathoGFAIR, name:IWC 2023-05-11 2024-06-05 58 58 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Taxonomic classification, Aggregation, Visualisation MIT +FASTQC-MULTIQC-Quality-Check_FastQ_Files https://usegalaxy.eu 0ec684b341ad172d https://usegalaxy.eu/published/workflow?id=0ec684b341ad172d BGGM, Microbiome, Amplicon, FASTQC, QualityCheck 2024-05-13 2024-05-17 8 8 multiqc, fastqc Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation +Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, IWC, name:Collection, name:microGalaxy 2022-11-29 2024-04-04 205 205 clustalw, regex1, tab2fasta, tp_sorted_uniq, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, regexColumn1, collection_column_join, Grouping1, Count1, tp_split_on_column, fasttree, tp_replace_in_column, Remove beginning1, tp_multijoin_tool, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, fasta2tab, Cut1, newick_display, ggplot2_heatmap, interactive_tool_jupyter_notebook, __FILTER_FAILED_DATASETS__ Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Mapping, Multiple sequence alignment, Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods) MIT +Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microGalaxy 2023-10-10 2024-03-15 128 128 __BUILD_LIST__, interactive_tool_jupyter_notebook +dada2 amplicon analysis pipeline - for paired en (release v0.1) https://usegalaxy.eu b483cf6a138d2372 https://usegalaxy.eu/published/workflow?id=b483cf6a138d2372 Matthias Bernt, UFZ Leipzig name:amplicon 2024-03-14 2024-03-14 1 1 dada2_dada, __APPLY_RULES__, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, dada2_seqCounts Variant calling, DNA barcoding MIT +Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microGalaxy 2023-09-25 2024-03-13 80 80 map_param_value, __FILTER_EMPTY_DATASETS__, Grep1, __BUILD_LIST__, __EXTRACT_DATASET__ +WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalMP, name:microGalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences Tag-based peptide identification, Target-Decoy, de Novo sequencing, Protein identification, Expression analysis +WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Cut1, dbbuilder, Remove beginning1, tp_cat, query_tabular, Filter1, peptide_shaker, msconvert, Grep1, Grouping1, filter_tabular, maxquant, ident_params, search_gui, fasta_cli, fasta_merge_files_and_filter_unique_sequences, fasta2tab Heat map generation, Statistical calculation, Visualisation, Protein quantification, Filtering, Principal component plotting, Formatting, Standardisation and normalisation, Imputation, Clustering +WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Cut1, dbbuilder, Remove beginning1, tp_cat, pepquery2, query_tabular, Filter1, Grouping1, uniprotxml_downloader, collapse_dataset, fasta_merge_files_and_filter_unique_sequences +WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalMP, name:microGalaxy 2023-12-14 2023-12-14 1 1 Cut1, maxquant, Grep1, Grouping1 Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microGalaxy, name:clinicalMP 2023-12-14 2023-12-14 1 1 Grep1, msstatstmt, unipept Prediction and recognition, Visualisation +MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wf Data retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction +MetaP https://usegalaxy.eu 01ac8bf9832789e2 https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 name:microgalaxy 2023-12-14 2023-12-14 1 1 maxquant Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +MetaT https://usegalaxy.eu 3733bcdf5b458be7 https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 name:microgalaxy 2023-12-14 2023-12-14 1 1 kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqc Sequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling +metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_stat Query and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification +metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_expand, metaquantome_sample, metaquantome_viz, metaquantome_filter, metaquantome_stat Query and retrieval, Functional clustering, Heat map generation, Differential protein expression analysis, Indexing, Visualisation, Principal component visualisation, Filtering, Statistical inference, Quantification +Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 query_tabular, sqlite_to_tabular, search_gui, peptide_shaker, unipept Prediction and recognition, Visualisation +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_grep_tool, collapse_dataset, lastz_wrapper_2, join1, mergeCols1, bedtools_complementbed, tp_sed_tool, Grep1, bedtools_intersectbed, random_lines1, cat1, Filter1, datamash_ops, Cut1, tp_cat, fasta_compute_length, bedtools_sortbed, addValue, tp_sort_header_tool, fasta_filter_by_length Mapping, Read mapping, Sequence alignment +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, Remove beginning1, tp_replace_in_line, multiqc, porechop, fastqc, kraken2, fastp, datamash_reverse Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Validation, Visualisation, Statistical calculation +Main Metatranscriptomics Analysis https://usegalaxy.eu 7a08ecdf23e0c7a3 https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep name:microGalaxy 2023-12-14 2023-12-14 0 0 MIT +Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 bandage_image, staramr_search, gfa_to_fa, nanoplot, PlasFlow, miniasm, racon, unicycler, minimap2 Aggregation, Mapping assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequence analysis, Scatter plot plotting, De-novo assembly +Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina Metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, Filter1, porechop, fastqc, kraken2, fastp, krakentools_kreport2krona Aggregation, Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Statistical calculation, Visualisation MIT +workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_cat, bowtie2, seqtk_subseq, ngsutils_bam_filter, megahit, filter_tabular, bamtools, cutadapt, random_lines1, fastqc, bg_uniq Sequence composition calculation, Data handling, Variant calling, Statistical calculation, Read pre-processing, Sequence alignment analysis, Sequence file editing, Genome assembly, Formatting, Sequence contamination filtering, Primer removal, Sequencing quality control, Sequence trimming, Read mapping +Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microGalaxy 2023-12-14 2023-12-14 0 0 bandage_image, bowtie2, collection_column_join, megahit, metaspades, quast, bandage_info, megahit_contig2fastg Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Read mapping, Visualisation +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, humann2_renorm_table, humann2, metaphlan2, humann2_regroup_table, metaphlan2krona Visualisation +Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut Metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 taxonomy_krona_chart, __UNZIP_COLLECTION__, interactive_tool_pavian, interactive_tool_phinch, est_abundance, kraken2, metaphlan, krakentools_kreport2krona, kraken_biom Phylogenetic tree analysis, Aggregation, Nucleic acid sequence analysis, Taxonomic classification, Statistical calculation, Visualisation MIT +Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 mothur_make_group, mothur_make_biom, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_pre_cluster, krona-text, mothur_count_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_make_shared, mothur_summary_seqs, mothur_merge_files Sequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding +Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microGalaxy 2023-12-14 2023-12-14 0 0 snippy, jbrowse Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation +Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microGalaxy 2023-12-14 2023-12-14 0 0 freebayes, Cut1, picard_MergeSamFiles, vcf2tsv, picard_MarkDuplicates, bwa_mem, bamFilter, bamleftalign, fastqc, vcffilter2 Sequence composition calculation, Generation, Data handling, Variant calling, Statistical calculation, Genome indexing, Sequence alignment, Sequence alignment analysis, Formatting, Sequencing quality control, Read mapping +Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microGalaxy 2023-12-14 2023-12-14 0 0 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_remove_groups, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_seq_error, mothur_tree_shared, mothur_cluster, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_get_groups, mothur_summary_single, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearch Sequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 Cut1, cat1, Filter1, bg_diamond, regexColumn1, rapidnj, bg_diamond_view, rbc_mafft, gops_intersect_1, tp_split_on_column, Add_a_column1, tab2fasta, collapse_dataset, join1 Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis +Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microGalaxy 2023-12-14 2023-12-14 0 0 multiqc, prokka, quast, fastqc, unicycler Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction +Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 list_organism, create_account, create_or_update, jbrowse, iframe Genome visualisation +Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microGalaxy 2023-12-14 2023-12-14 0 0 prokka, jbrowse Genome annotation, Coding region prediction, Genome visualisation, Gene prediction +Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_easyjoin_tool, regex1, tp_text_file_with_recurring_lines, gff2bed1, jbrowse, tbl2gff3, tab2fasta, tp_cut_tool, join1, bandage_image, staramr_search, Grep1, circos_interval_to_tile, PlasFlow, tp_split_on_column, bg_column_arrange_by_header, minimap2, medaka_consensus_pipeline, Filter1, tp_head_tool, trimmomatic, circos_wiggle_to_scatter, ncbi_blastn_wrapper, circos, Add_a_column1, flye, fasta2tab, fasta_compute_length, tp_cat, Cut1, circos_gc_skew, nanoplot, prokka, deeptools_bam_coverage, regex_replace, tp_sort_header_tool Sequence analysis, Variant calling, Mapping assembly, Sequence assembly, Gene prediction, Sequence visualisation, Cross-assembly, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Genome visualisation, Coding region prediction, Genome annotation, Base-calling, Scatter plot plotting, De-novo assembly +Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 raxml, interactive_tool_rstudio Phylogenetic tree analysis, Sequence analysis +From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 tp_cat, tb_variant_filter, bcftools_consensus, snp_dists, snp_sites +From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 __MERGE_COLLECTION__, tb_variant_filter, trimmomatic, snippy Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation +From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microGalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, tp_cat, addName, tp_sed_tool, tp_replace_in_line, samtools_view, tp_grep_tool, __MERGE_COLLECTION__ Antimicrobial resistance prediction +M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microGalaxy 2023-12-14 2023-12-14 0 0 tb_profiler_profile, tb_variant_filter, trimmomatic, multiqc, jbrowse, tbvcfreport, snippy, fastqc, kraken2 Sequence composition calculation, Phylogenetic tree generation, Variant calling, Validation, Phylogenetic tree visualisation, Statistical calculation, Antimicrobial resistance prediction, Sequencing quality control, Genome visualisation, Taxonomic classification MIT +Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microGalaxy, HPylori 2023-12-13 2023-12-13 2 2 freebayes, tp_awk_tool, bowtie2, vcf2tsv, snpSift_filter, bcftools_norm, bcftools_view Variant calling, Statistical calculation, Read mapping +Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microGalaxy, HPylori 2023-10-27 2023-12-13 13 13 freebayes, tp_cat, bowtie2, vcf2tsv, collection_element_identifiers, samtools_coverage, collapse_dataset, bcftools_norm, samtools_depth Variant calling, Statistical calculation, Read mapping +MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 MGnify_Amplicon_Showcase, name:microGalaxy 2023-12-12 2023-12-13 1 1 taxonomy_krona_chart, tp_awk_tool, query_tabular, cmsearch_deoverlap, gops_concat_1, biom_convert, infernal_cmsearch, bedtools_getfastabed, mapseq, bedtools_maskfastabed Formatting, Nucleic acid feature detection, k-mer counting, Alignment, Comparison, Mapping, Visualisation +MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 MGnify_Amplicon_Showcase, name:microGalaxy 2023-12-13 2023-12-13 1 1 __UNZIP_COLLECTION__, trimmomatic, fastq_to_fasta_python, multiqc, cshl_fasta_formatter, iuc_pear, prinseq, fastqc, tp_find_and_replace, fastp, fastq_dump Sequence composition calculation, Data handling, Validation, Sequence merging, Statistical calculation, Read pre-processing, Sequence contamination filtering, Sequencing quality control, Sequence trimming + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microGalaxy 2021-11-10 2023-12-07 2 2 featurecounts, bowtie2, multiqc Validation, Sequencing quality control, Read summarisation, Read mapping, RNA-Seq quantification +Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microGalaxy 2021-11-01 2023-12-07 72 72 dbbuilder, translate_nucleotides, bowtie2, cat1, bg_diamond, cd_hit, kofamscan, metagene_annotator, bg_diamond_makedb, multiqc, megahit, bedtools_getfastabed, quast, fastqc, metaeuk_easy_predict, eggnog_mapper Sequence clustering, Information extraction, Query and retrieval, Homology-based gene prediction, Visualisation, Genome assembly, Sequencing quality control, Genome annotation, Mapping, Sequence analysis, Sequence composition calculation, Sequence assembly validation, Sequence annotation, Validation, Statistical calculation, Fold recognition, Gene functional annotation, Sequence alignment analysis, Read mapping +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microGalaxy 2021-11-01 2023-12-07 51 51 trimmomatic, multiqc, fastqc Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microGalaxy 2022-06-29 2023-12-07 28 28 recentrifuge, bowtie2, seq_filter_by_id, filter_tabular, kraken2, fastq_to_tabular Taxonomic classification, Expression analysis, Read mapping, Cross-assembly +Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microGalaxy 2022-09-03 2023-12-07 18 18 recentrifuge, interactive_tool_phinch, kraken2, maaslin2, kraken_biom Filtering, Standardisation and normalisation, Taxonomic classification, Statistical calculation, Expression analysis, Visualisation, Cross-assembly +Main Metatranscriptomics Analysis 24.08.2023 https://usegalaxy.eu 81033ff723b9f22d https://usegalaxy.eu/published/workflow?id=81033ff723b9f22d microbiome 2023-08-24 2023-11-07 6 6 +pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:functionalProfiling 2023-07-07 2023-07-07 3 3 Cut1, humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, tp_find_and_replace, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT + pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microGalaxy, name:metatranscriptomics, name:AdaptedASiam, name:communityProfiling 2023-06-30 2023-07-06 3 3 Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlan Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editing MIT + pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microGalaxy, name:AdaptedASiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2023-07-06 2 2 __FLATTEN__, multiqc, bg_sortmerna, fastq_paired_end_interlacer, cutadapt, fastqc Sequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming MIT +Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification https://usegalaxy.eu 3f0b104a74acf869 https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869 Engy Nasr, Bérénice Batut microbiome, nanopore 2023-01-16 2023-05-30 8 8 clair3, bcftools_consensus, bcftools_norm, snpSift_filter, minimap2, snpSift_extractFields Variant calling, Pairwise sequence alignment MIT +Pathogen-Detection-Nanopore-Gene-based-pathogenic-Identification https://usegalaxy.eu 2b888e200dfd91bc https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc Engy Nasr, Bérénice Batut microbiome, nanopore 2023-01-10 2023-05-30 20 20 mlst, bandage_image, Cut1, medaka_consensus_pipeline, cat1, add_line_to_file, abricate, tab2fasta, compose_text_param, tp_find_and_replace, tp_replace_in_column, flye, fasta2tab Mapping assembly, Variant calling, Sequence assembly, Cross-assembly, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Sequence assembly visualisation, Base-calling, De-novo assembly MIT +Pathogen Detection-Nanopore-Taxonomy-Profiling-and-Visualization https://usegalaxy.eu a0ea6fc756dd17ea https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea Engy Nasr, Bérénice Batut microbiome, nanopore 2023-02-02 2023-05-30 4 4 kraken2, interactive_tool_phinch, kraken_biom Taxonomic classification MIT +Pathogen-Detection-Nanopore-Taxonomy-Profiling-and-Visualization-with-krona https://usegalaxy.eu ed2df13cfbc86b99 https://usegalaxy.eu/published/workflow?id=ed2df13cfbc86b99 Engy Nasr, Bérénice Batut microbiome, nanopore 2023-02-17 2023-05-30 6 6 kraken2, krakentools_kreport2krona, krona-text Taxonomic classification, Aggregation, Visualisation MIT +Pathogen-Detection-Nanopore-Pre-Processing https://usegalaxy.eu 889f2782ad82bd69 https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69 Bérénice Batut, Engy Nasr microbiome, nanopore 2023-02-02 2023-05-30 6 6 porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastp Sequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +Resistome workflow Pig Nov2021 (imported from uploaded file) https://usegalaxy.eu 25850714d13f0b0f https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f Metagenomics, Resistome 2023-05-22 2023-05-23 0 0 bowtie2, resistome_analyzer, samtools_sort, bam_to_sam, rarefaction_analyzer, snpfinder, XY_Plot_1, fastp Sequencing quality control, Sequence contamination filtering, Read mapping +ASaiM-MT:metaphlan https://usegalaxy.eu ed0ad728cf21702b https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b ASaiM 2023-05-17 2023-05-17 3 3 taxonomy_krona_chart, metaphlan2, graphlan, format_metaphlan2_output, export2graphlan, graphlan_annotate, fastq_paired_end_interlacer, metaphlan2krona Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Formatting, Conversion, Taxonomic classification, Phylogenetic tree editing +Training: 16S rRNA RNIMU https://usegalaxy.eu dadca1020f586338 https://usegalaxy.eu/published/workflow?id=dadca1020f586338 metagenomics 2023-04-24 2023-04-27 8 8 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, mothur_make_contigs, mothur_classify_otu, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, mothur_tree_shared, mothur_chimera_vsearch, mothur_venn, mothur_make_biom, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, newick_display, mothur_count_groups, mothur_make_shared, mothur_rarefaction_single Sequence clustering, Phylogenetic tree generation, Phylogenetic analysis, Visualisation, Sequence read processing, Phylogenetic tree analysis, Sequencing quality control, Taxonomic classification, Phylogenetic tree reconstruction, DNA barcoding +MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Heat map generation, Statistical calculation, Visualisation, Protein quantification, Principal component plotting, Standardisation and normalisation, Imputation, Clustering +MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 coverm_genome, tp_cat, fraggenescan, fasplit, tp_awk_tool, kofamscan, hmmer_hmmscan, tp_grep_tool, quast, interproscan, trim_galore, fastqc, sort1, maxbin2, cat_bins, coverm_contig, checkm_lineage_wf Data retrieval, Sequence assembly, Sequence generation, Visualisation, Protein feature detection, Local alignment, Conversion, Sequencing quality control, Format validation, Coding region prediction, Database search, Taxonomic classification, Sequence analysis, Sequence motif recognition, Sequence trimming, Multiple sequence alignment, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequence database search, Read pre-processing, Primer removal, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene functional annotation, Gene prediction +Pox Virus Illumina Amplicon Workflow from half-genomes (release v0.1) https://usegalaxy.eu b77e3b08092fa73e https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e Viktoria Isabel Schwarz, Wolfgang Maier pox, virology 2023-03-02 2023-03-02 1 1 ivar_trim, qualimap_bamqc, bwa_mem, compose_text_param, __ZIP_COLLECTION__, Grep1, tp_sed_tool, samtools_stats, __SORTLIST__, samtools_merge, __APPLY_RULES__, __FLATTEN__, ivar_consensus, datamash_ops, fastp, fasta_compute_length, Cut1, param_value_from_file, tp_cat, collection_element_identifiers, __FILTER_FAILED_DATASETS__, samtools_view, multiqc, split_file_to_collection, EMBOSS: maskseq51 Generation, Validation, Genome indexing, Sequence alignment, Sequence alignment analysis, Sequence contamination filtering, Local alignment, Sequencing quality control, Sequence analysis, Read mapping, Global alignment MIT +MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 kallisto_quant, __UNZIP_COLLECTION__, collection_column_join, bg_sortmerna, trim_galore, fastqc Sequence composition calculation, Sequence similarity search, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming, Gene expression profiling +Nanopore Datasets - Pre-Processing https://usegalaxy.eu 57d3109f32defa3b https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b , , Bérénice Batut, , Engy Nasr microbiome, nanopore 2022-08-07 2023-01-29 71 71 porechop, nanoplot, multiqc, seq_filter_by_id, filter_tabular, fastqc, kraken2, fastp Sequence composition calculation, Validation, Statistical calculation, Box-Whisker plot plotting, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Scatter plot plotting MIT +Bacterial genome assembly - IZSPB https://usegalaxy.eu 37da7b42cb063a3a https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a assembly, bacterial, genome 2021-07-27 2022-12-03 18 18 mlst, spades, abricate, multiqc, prokka, quast, abricate_summary, fastp Sequence assembly validation, Validation, Visualisation, Genome assembly, Antimicrobial resistance prediction, Multilocus sequence typing, Sequence contamination filtering, Sequencing quality control, Coding region prediction, Genome annotation, Gene prediction +16S rDNA microbial analisys + MUSCLE mothur https://usegalaxy.eu 6d06bd22f206e176 https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176 16S, mothur, microbial, microbiome, OTU, Cluster, Rarefaction 2021-08-09 2022-07-29 8 8 mothur_chimera_uchime, mothur_get_oturep, mothur_unique_seqs, mothur_rarefaction_single, mothur_dist_seqs, mothur_remove_seqs, muscle, mothur_cluster Sequence clustering, Phylogenetic analysis, Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding +Metatranscriptomics-WF3: Functional Information (quick) https://usegalaxy.eu 5ce8a472e6e95c60 https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60 metagenomics 2021-05-25 2021-11-09 8 8 humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis +Metatranscriptomics-WF3: Functional Information https://usegalaxy.eu 23dd2253da51e22e https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e metagenomics 2021-05-25 2021-11-09 6 6 humann_unpack_pathways, combine_metaphlan2_humann2, Grep1, humann, humann_renorm_table, humann_split_stratified_table, humann_regroup_table, humann_rename_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis +Metatranscriptomics - analyze human RNA-seq data with Kraken (imported from uploaded file) https://usegalaxy.eu ee0005a5487653ba https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba None metatranscriptomics, Kraken, RNA-seq, microbiome 2021-10-18 2021-10-18 2 2 taxonomy_krona_chart, Kraken2Tax, picard_SamToFastq, trimmomatic, samtools_view, bwa, fastqc, kraken2 Sequence composition calculation, Generation, Statistical calculation, Genome indexing, Sequence alignment, Visualisation, Formatting, Sequencing quality control, Taxonomic classification, Read mapping +Taxonomic and functional community profiling of raw metagenomic shotgun data workflow https://usegalaxy.eu a8f829deb69b30ab https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab asaim 2021-06-22 2021-06-24 14 14 taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann_unpack_pathways, Grep1, format_metaphlan2_output, graphlan_annotate, combine_metaphlan2_humann2, humann, bg_sortmerna, export2graphlan, humann_regroup_table, fastqc, Cut1, humann2_genefamilies_genus_level, graphlan, multiqc, humann_renorm_table, metaphlan, humann_rename_table Sequence similarity search, Phylogenetic analysis, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Nucleic acid sequence analysis, Species frequency estimation, Sequence comparison +Metatranscriptomcis-WF2: Community Profile https://usegalaxy.eu 19de5cbae7f48103 https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103 metagenomics 2021-05-25 2021-05-25 2 2 Cut1, taxonomy_krona_chart, graphlan, export2graphlan, graphlan_annotate, metaphlan Phylogenetic inference, Phylogenetic tree visualisation, Visualisation, Phylogenetic tree analysis, Conversion, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree editing +Metatranscriptomics-WF1: Preprocessing https://usegalaxy.eu f6e8a63283262518 https://usegalaxy.eu/published/workflow?id=f6e8a63283262518 metagenomics 2021-05-25 2021-05-25 2 2 bg_sortmerna, multiqc, fastq_paired_end_interlacer, cutadapt, fastqc Sequence composition calculation, Sequence similarity search, Validation, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence comparison, Sequence trimming +ASaiM-MT https://usegalaxy.eu dfc2c53ac3103eff https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff ASaiM 2020-12-04 2020-12-04 1 1 taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, fastq_paired_end_interlacer, cutadapt, humann2, Grep1, format_metaphlan2_output, graphlan_annotate, Grouping1, humann2_unpack_pathways, metaphlan2krona, metaphlan2, combine_metaphlan2_humann2, bg_sortmerna, export2graphlan, fastqc, humann2_renorm_table, humann2_genefamilies_genus_level, graphlan, multiqc, tp_sort_header_tool Sequence similarity search, Phylogenetic tree visualisation, Visualisation, Conversion, Sequencing quality control, Taxonomic classification, Sequence trimming, Phylogenetic tree editing, Sequence composition calculation, Phylogenetic inference, Statistical calculation, Validation, Read pre-processing, Primer removal, Sequence alignment analysis, Formatting, Sequence comparison +Workflow 3: Functional Information [Metatranscriptomics] https://usegalaxy.eu c817aefc77933d79 https://usegalaxy.eu/published/workflow?id=c817aefc77933d79 metagenomics 2020-07-13 2020-07-14 1 1 humann2_renorm_table, humann2, humann2_unpack_pathways, group_humann2_uniref_abundances_to_go +0_Short-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu 374797e58377c40f https://usegalaxy.eu/published/workflow?id=374797e58377c40f Assembly, Unicycler, StarAMR, Bacterial, Prokka, Short-Read, Illumina 2020-06-24 2020-06-24 4 4 bandage_image, staramr_search, multiqc, prokka, quast, bandage_info, fastqc, unicycler, fastp Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Genome assembly, Sequence contamination filtering, Sequencing quality control, Sequence assembly visualisation, Coding region prediction, Genome annotation, Gene prediction +0_Hybrid_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu ecf48fa50af560a0 https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0 Hybrid, Assembly, ONT, Unicycler, StarAMR, Bacterial, Prokka 2020-06-24 2020-06-24 13 13 filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, multiqc, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, fastqc, unicycler, fastp, minimap2 Aggregation, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Pairwise sequence alignment, Scatter plot plotting, Gene prediction +0_Long-read_assembly-_-_-Filter-Unicycler-AMR-annotation_(24-06-2020) https://usegalaxy.eu ea485dbabc76488d https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d Assembly, ONT, Unicycler, StarAMR, Bacterial, Prokka, Coverage 2020-06-24 2020-06-24 3 3 filtlong, bandage_image, Cut1, staramr_search, bedtools_genomecoveragebed, nanoplot, prokka, quast, bandage_info, Summary_Statistics1, unicycler, minimap2 Aggregation, Sequence assembly validation, Visualisation, Filtering, Genome assembly, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Mapping, Scatter plot plotting, Gene prediction +MetaGalaxy https://usegalaxy.eu 5826e573b6f93762 https://usegalaxy.eu/published/workflow?id=5826e573b6f93762 Long_Read, Metagenomics, Assembly, AMR, Taxonomy, Gene_Annotation, Long_Read 2020-01-22 2020-04-21 1 1 Cut1, filtlong, bandage_image, mlst, abricate, nanoplot, Krona, racon, prokka, jbrowse, quast, bandage_info, kraken2, meta_flye, minimap2 Sequence assembly validation, Mapping assembly, Visualisation, Taxonomic classification, Filtering, Genome assembly, Multilocus sequence typing, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequencing quality control, Coding region prediction, Genome annotation, Genome visualisation, Pairwise sequence alignment, Scatter plot plotting, Gene prediction +MetaGalaxy (4x polishing w Racon) https://usegalaxy.eu a337bfb2eb1e583f https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f Nanopore, Metagenomics, ONT 2020-01-31 2020-02-10 4 4 Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flye Mapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction +MetaGalaxy https://usegalaxy.eu a84bac86ec183d46 https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46 Nanopore, Metagenomics, ONT 2020-01-24 2020-02-10 8 8 Cut1, filtlong, taxonomy_krona_chart, bandage_image, mlst, minimap2, abricate, nanoplot, racon, jbrowse, prokka, quast, bandage_info, kraken2, flye Mapping assembly, Visualisation, Cross-assembly, Genome assembly, Multilocus sequence typing, Pairwise sequence alignment, Sequencing quality control, Coding region prediction, Taxonomic classification, Genome annotation, De-novo assembly, Sequence assembly validation, Filtering, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Genome visualisation, Scatter plot plotting, Gene prediction +16S microbial analysis (Mothur) https://usegalaxy.eu ce21961260fe4351 https://usegalaxy.eu/published/workflow?id=ce21961260fe4351 Metagenomics, Mothur, 16S 2018-09-22 2018-09-22 1 1 mothur_taxonomy_to_krona, taxonomy_krona_chart, mothur_classify_seqs, mothur_heatmap_bin, mothur_dist_shared, mothur_align_seqs, mothur_filter_seqs, mothur_rarefaction_single, mothur_count_seqs, mothur_remove_lineage, mothur_screen_seqs, mothur_summary_seqs, mothur_sub_sample, collapse_dataset, mothur_make_contigs, mothur_pcoa, mothur_classify_otu, mothur_get_oturep, mothur_unique_seqs, mothur_pre_cluster, mothur_cluster_split, fasttree, mothur_venn, mothur_heatmap_sim, XY_Plot_1, mothur_remove_seqs, mothur_summary_single, mothur_count_groups, mothur_dist_seqs, mothur_make_shared, mothur_chimera_vsearch Sequence clustering, Phylogenetic analysis, Phylogenetic tree generation (from molecular sequences), Visualisation, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding, Phylogenetic tree generation (maximum likelihood and Bayesian methods) +ASaiM - Metagenomic assembly with MetaSPAdes https://usegalaxy.eu 579ff83177c5ee09 https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 ASaiM 2018-01-17 2018-08-03 3 3 bowtie2, valet, multiqc, metaspades, quast, trim_galore, fastqc Sequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping +ASaiM - Metagenomic assembly with MEGAHIT https://usegalaxy.eu 1524b189069b42a5 https://usegalaxy.eu/published/workflow?id=1524b189069b42a5 ASaiM 2018-01-17 2018-08-03 4 4 bowtie2, valet, multiqc, megahit, quast, trim_galore, fastqc Sequence composition calculation, Sequence assembly validation, Validation, Sequence assembly, Statistical calculation, Visualisation, Read pre-processing, Primer removal, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence trimming, Read mapping +ASaiM - Shotgun workflow for paired-end data collection https://usegalaxy.eu 329cf724a21f13ec https://usegalaxy.eu/published/workflow?id=329cf724a21f13ec ASaiM 2018-04-30 2018-04-30 1 1 +Shotgun workflow for paired-end data (imported from uploaded file) https://usegalaxy.eu 358db17bfc1ee330 https://usegalaxy.eu/published/workflow?id=358db17bfc1ee330 ASaiM 2018-01-29 2018-04-30 0 0 fastq_join +ASaiM - Shotgun workflow for single-end data collection https://usegalaxy.eu 1c3adfc77a138ef6 https://usegalaxy.eu/published/workflow?id=1c3adfc77a138ef6 ASaiM 2018-01-29 2018-04-30 2 2 +QIIME - Illumina Overview tutorial (imported from uploaded file) https://usegalaxy.eu 3acfb87be6db2303 https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303 ASaiM 2018-01-17 2018-01-17 0 0 qiime_pick_open_reference_otus, qiime_split_libraries_fastq, qiime_core_diversity, qiime_validate_mapping_file, qiime_count_seqs Phylogenetic analysis, Visualisation, Sequencing quality control, Taxonomic classification, Demultiplexing +EBI Metagenomics workflow (3.0) (imported from uploaded file) https://usegalaxy.eu 58955868b504c60d https://usegalaxy.eu/published/workflow?id=58955868b504c60d ASaiM 2018-01-17 2018-01-17 0 0 hmmer_hmmsearch, cshl_fastq_to_fasta, tp_awk_tool, tp_cat, fraggenescan, trimmomatic, seq_filter_by_id, hmmer_hmmbuild, interproscan, qiime_pick_closed_reference_otus Data retrieval, Phylogenetic analysis, Sequence generation, Visualisation, Protein feature detection, Conversion, Sequencing quality control, Format validation, Database search, Taxonomic classification, Sequence motif recognition, Multiple sequence alignment, Demultiplexing, Statistical calculation, Sequence database search, Formatting, Sequence profile generation, Probabilistic sequence generation, Gene prediction diff --git a/communities/proteomics/resources/tools.tsv b/communities/proteomics/resources/tools.tsv deleted file mode 100644 index 890b393f..00000000 --- a/communities/proteomics/resources/tools.tsv +++ /dev/null @@ -1,1476 +0,0 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq 2022-05-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 307 307 80 80 8 8 3 3 3 3 1 1 318 318 84 84 False -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 False -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source 2015-11-17 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 474 2914 132 163 0 0 0 0 0 0 0 0 474 2914 132 163 False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 False -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 False -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq 2021-10-08 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49465 49465 281 281 0 0 0 0 0 0 0 0 49465 49465 281 281 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 False -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -add_input_name_as_column addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column 2020-03-24 mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 76834 86002 227 246 20174 20953 312 395 11 11 2 2 97019 106966 541 643 False -add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file 2020-11-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 15933 15933 378 378 1736 1736 214 214 380 380 28 28 18049 18049 620 620 False -add_value addValue Add a value as a new column. To update Text Manipulation add_value 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 37860 374587 1293 1610 17588 293713 1243 6197 3873 4397 202 229 59321 672697 2738 8036 False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro 2017-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 False -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 False -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 False -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 False -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services 2020-06-29 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 3600 3760 883 911 6 6 4 4 0 0 0 0 3606 3766 887 915 False -appendfdr append_fdr To update appendfdr 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 False -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning 2020-10-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 False -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services 2017-08-11 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 False -astropytools astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations To update https://github.com/astropy/astropy Astronomy astropytools 2023-04-11 volodymyrss https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0.1.0+galaxy0 astropy 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 5 5 0 0 0 0 0 0 0 0 13 13 5 5 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 False -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx 2015-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 131 15 20 329 785 50 210 0 0 0 0 412 916 65 230 False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 False -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 False -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 False -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 False -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 False -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source 2022-03-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 False -basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 226 308 27 35 2615 45557 302 2284 482 522 32 36 3323 46387 361 2355 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil 2019-05-22 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 306 311 82 83 467 467 99 99 0 0 0 0 773 778 181 182 False -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers batched_lastz 2024-04-30 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 5 5 0 0 0 0 123 123 5 5 False -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 False -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 False -bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://www.encodeproject.org/software/bedgraphtobigwig/ Convert Formats bbgbigwig 2024-06-14 iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig 0.1 ucsc-bedgraphtobigwig 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 7 7 175 175 26 26 0 0 0 0 217 217 33 33 False -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 False -bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.21 Data handling, Variant calling DNA polymorphism, GWAS study, Genotyping experiment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 False -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 2023-08-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 33 33 9 9 0 0 0 0 0 0 0 0 33 33 9 9 False -beacon2-import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://pypi.org/project/beacon2-import/ Variant Analysis Beacon2_Import 2024-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import 2.2.4 beacon2-import 2.2.4 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 12 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 7 7 0 0 0 0 0 0 0 0 22 22 7 7 False -beagle beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle 2021-07-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 28 28 0 0 0 0 0 0 0 0 88 88 28 28 False -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 False -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed 2023-08-08 iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 36 36 181 181 62 62 0 0 0 0 274 274 98 98 False -bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 Mapping Genomics 37 37 37 37 37 37 37 37 0 0 0 0 0 0 0 0 37 6 37 0 0 37 0 0 0 37 0 0 0 0 0 0 37 37 37 0 916111 962278 13235 14525 407944 647621 25849 41751 84008 89233 2486 2832 1408063 1699132 41570 59108 False -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 False -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 False -bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph 2015-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph 2021-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 469 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig 2018-09-25 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 469 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers 2018-04-23 iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.9 python-bioext 0.21.9 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 17413 17413 822 822 15349 15349 2020 2020 2 2 1 1 32764 32764 2843 2843 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter 2019-03-15 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 False -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 False -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast 2022-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 738 738 151 151 0 0 0 0 2 2 1 1 740 740 152 152 False -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 False -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 False -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 False -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 False -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 False -bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 2018-04-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 Read mapping Mapping, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 397893 427447 12133 13176 577209 903193 33086 52020 60105 67495 3779 4271 1035207 1398135 48998 69467 False -bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 24164 25149 1320 1480 17537 203397 1330 17491 15654 15992 291 351 57355 244538 2941 19322 False -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -breseq breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq 2019-10-21 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.39.0 Polymorphism detection Sequencing, Sequence analysis, DNA mutation 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 2976 2976 98 98 0 0 0 0 884 884 70 70 3860 3860 168 168 False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 False -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 False -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 False -bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa 2017-11-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 2 976935 1017671 13526 14401 474702 681286 32627 47624 79802 87191 4219 4954 1531439 1786148 50372 66979 False -bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 2021-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 Sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 56619 56619 2324 2324 36631 36631 2808 2808 18121 18121 713 713 111371 111371 5845 5845 False -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 False -c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s 2021-04-13 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.3.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 234 234 11 11 4 4 4 4 92 92 3 3 330 330 18 18 False -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 False -cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads 2021-06-19 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 1 1 0 0 0 0 0 0 0 0 52 52 1 1 False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param 2021-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1393 1393 10 10 0 0 0 0 0 0 0 0 1393 1393 10 10 False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu 2018-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 De-novo assembly Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13360 14618 1383 1444 0 0 0 0 3542 3542 385 385 16902 18160 1768 1829 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 175 28 39 0 0 0 0 0 0 0 0 88 175 28 39 False -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis 2021-09-01 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 218 218 17 17 0 0 0 0 0 0 0 0 218 218 17 17 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm 2021-06-15 climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 2 2 0 0 0 0 0 0 0 0 14 14 2 2 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services 2018-11-05 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -change_case ChangeCase Convert column case. To update Text Manipulation change_case 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 10606 12531 2204 2547 9044 17167 1748 2394 923 938 240 245 20573 30636 4192 5186 False -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 False -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca 2024-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.10 0 0 8 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 727 727 76 76 0 0 0 0 0 0 0 0 727 727 76 76 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 False -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 False -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos 2020-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 Sequence visualisation 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 26265 26265 2483 2483 31332 31332 3535 3535 26359 26359 999 999 83956 83956 7017 7017 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 False -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 False -cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 513 813 18 35 2406 30579 156 1547 1353 1393 17 20 4272 32785 191 1602 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 False -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 False -cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.1.0 cnv-vcf2json 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit 2023-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 Variant calling 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 618 618 177 177 0 0 0 0 0 0 0 0 618 618 177 177 False -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 False -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 False -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 False -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 False -collection_column_join collection_column_join Column Join on Collections To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join Text Manipulation collection_column_join 2016-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 23979 25337 3827 4011 21671 25163 4645 5045 2939 3036 688 701 48589 53536 9160 9757 False -collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers Text Manipulation collection_element_identifiers 2018-06-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6905 7102 1620 1630 7761 7761 1897 1897 1157 1157 243 243 15823 16020 3760 3770 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -column_arrange_by_header bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header 2015-03-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5356 5636 446 484 2026 2026 375 375 1400 1531 117 138 8782 9193 938 997 False -column_maker Add_a_column1 Compute an expression on every row To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker Text Manipulation column_maker 2019-06-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2940752 3907183 5422 6121 263254 737503 6095 13728 96478 97667 884 974 3300484 4742353 12401 20823 False -column_order_header_sort column_order_header_sort Sort Column Order by heading To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort Text Manipulation column_order_header_sort 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3735 3891 268 297 1923 1923 381 381 0 0 0 0 5658 5814 649 678 False -column_remove_by_header column_remove_by_header Remove columns by header To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header Text Manipulation column_remove_by_header 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8331 8917 613 662 5206 5206 716 716 1976 1976 27 27 15513 16099 1356 1405 False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 False -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 False -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 False -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 False -complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 187 233 15 20 495 4810 165 836 405 451 7 7 1087 5494 187 863 False -compose_text_param compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param 2019-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 45827 45831 689 691 7721 7721 303 303 1481 1481 121 121 55029 55033 1113 1115 False -compress_file compress_file Compress files. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file Text Manipulation compress_file 2022-02-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6343 6343 290 290 3674 3674 286 286 11832 11832 59 59 21849 21849 635 635 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 575128 575441 694 783 43420 85345 629 3508 19330 19418 104 117 637878 680204 1427 4408 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets 2019-04-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 4822 4824 613 614 1317 1317 204 204 3088 3795 252 289 9227 9936 1069 1107 False -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired 2019-12-16 nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 False -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2173 28 368 195 205 8 8 242 2378 36 376 False -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 23589 28986 1061 1200 23507 160693 2302 8699 5413 6446 251 329 52509 196125 3614 10228 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler 2018-12-07 lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.21 4 0 5 0 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 170 170 26 26 195 195 39 39 0 0 0 0 365 365 65 65 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1560 1725 43 58 4328 44209 193 2113 283 316 16 18 6171 46250 252 2189 False -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 False -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 False -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 False -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies Up-to-date http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap 2017-07-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.7.0 crossmap 0.7.0 5 0 6 0 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 2182 2182 331 331 5251 5251 903 903 0 0 0 0 7433 7433 1234 1234 False -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 False -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 False -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk 2019-08-27 nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cta cta_astro_tool Basic simulation of CTA telescope observations using gammapy package To update Astronomy cta_astro_tool 2024-04-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0.0.1+galaxy0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 False -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 False -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 False -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 False -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 False -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 False -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 False -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 False -cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular 2014-12-22 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 1208 43 97 1334 2683 101 479 0 0 0 0 2222 3891 144 576 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1973168 2034965 11939 12833 352364 803522 12967 30199 128777 133584 2341 2572 2454309 2972071 27247 45604 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Up-to-date https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv 2020-09-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 2.1.1 cutesv 2.1.1 Split read mapping, Genotyping, Structural variation detection Sequencing, Computer science 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 260 260 43 43 0 0 0 0 119 119 8 8 379 379 51 51 False -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 173 280 41 83 0 0 0 0 173 280 41 83 False -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 False -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga 2016-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation 2015-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 1 3 3 0 0 1 0 0 0 1 0 0 0 0 0 0 3 3 3 0 748586 760943 7066 7307 98089 112831 5306 6131 16235 16317 2161 2171 862910 890091 14533 15609 False -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 False -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 False -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -deepvariant deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant 2021-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2561 2561 325 325 2916 2916 460 460 0 0 0 0 5477 5477 785 785 False -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 False -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 False -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly 2020-10-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.3.1 Indel detection, Structural variation detection, Genotyping Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 1451 1451 288 288 0 0 0 0 0 0 0 0 1451 1451 288 288 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator 2013-11-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 69 26 30 0 304 0 133 0 0 0 0 59 373 26 163 False -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 False -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 False -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 False -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 False -diff diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff 2020-03-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 362 362 99 99 23 23 17 17 0 0 0 0 385 385 116 116 False -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 False -diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq Up-to-date http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2018-04-07 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 3.12.0 bioconductor-diffbind 3.12.0 Differential binding analysis ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7092 7663 606 652 14367 18624 1360 1916 1477 1640 69 84 22936 27927 2035 2652 False -diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -digestdb digestdb To update digestdb 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -directag_and_tagrecon To update directag_and_tagrecon 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 False -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot 2022-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver 2022-12-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 False -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools 2016-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.1 six 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 406 133 163 1421 1421 547 547 0 0 0 0 1697 1827 680 710 False -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta 2022-10-16 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4495 4495 111 111 0 0 0 0 0 0 0 0 4495 4495 111 111 False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa 2022-11-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload 2020-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.3 ena-upload-cli 0.7.4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 366 366 41 41 0 0 0 0 1302 1302 14 14 1668 1668 55 55 False -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch 2017-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1989 2302 367 453 0 0 0 0 0 0 0 0 1989 2302 367 453 False -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 False -ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep 2022-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 112.0 ensembl-vep 113.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3051 3051 171 171 0 0 0 0 0 0 0 0 3051 3051 171 171 False -eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie 2021-12-30 climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 4 4 0 0 0 0 0 0 0 0 45 45 4 4 False -epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg 2018-03-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 160 252 17 21 0 0 0 0 0 0 0 0 160 252 17 21 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability 2019-05-03 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 336 39 40 0 0 0 0 0 0 0 0 232 336 39 40 False -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 False -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 False -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster 2016-01-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 False -extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna 2016-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 9409 12735 813 923 20180 259099 2072 11791 168 611 20 63 29757 272445 2905 12777 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 False -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 False -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 False -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates 2020-10-21 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 264 264 69 69 34 34 11 11 103 103 1 1 401 401 81 81 False -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf 2023-01-11 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 385 385 46 46 587 587 107 107 58 58 5 5 1030 1030 158 158 False -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 False -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 False -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 False -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko 2018-04-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6690 8818 554 612 0 0 0 0 0 0 0 0 6690 8818 554 612 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -find_subsequences bg_find_subsequences To update find_subsequences 2015-03-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 784 69 79 2820 3047 323 361 20 20 1 1 3394 3851 393 441 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 589 731 51 63 2445 32847 304 2549 1214 1294 15 22 4248 34872 370 2634 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -footprint footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint 2017-04-18 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 5 5 0 0 0 0 0 0 0 0 57 57 5 5 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 False -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 False -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Up-to-date https://github.com/ekg/freebayes Variant Analysis freebayes 2017-01-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.8 freebayes 1.3.8 Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 149715 171093 8158 8794 144708 256315 15996 25107 19156 21936 2251 2571 313579 449344 26405 36472 False -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec 2020-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk Copy number estimation, Variant calling, Genome alignment Oncology, Human genetics, Data mining 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 748 748 91 91 0 0 0 0 12 12 1 1 760 760 92 92 False -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 False -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox 2018-06-05 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 2019-07-31 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution 2019-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 578 578 34 34 0 0 0 0 578 578 34 34 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 2021-12-29 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 2019-10-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3463 3463 452 452 9040 9040 1639 1639 0 0 0 0 12503 12503 2091 2091 False -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp 2017-06-23 iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 False -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 False -genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta 2020-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 4 4 2 2 221 2905 23 279 0 0 0 0 225 2909 25 281 False -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 Variant Analysis genehunter_modscore 2017-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 False -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services 2023-04-07 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.16 genoboo 0.4.16 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 False -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 660 104 197 0 0 0 0 445 660 104 197 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 False -genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich 2019-07-05 iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3534 3577 402 405 2840 2840 419 419 571 571 31 31 6945 6988 852 855 False -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage 2018-06-13 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3768 325011 1462 2044 9350 242043 2201 6583 787 1070 119 146 13905 568124 3782 8773 False -get_hrun get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 False -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9664 9775 763 765 5623 5623 493 493 1000 1000 135 135 16287 16398 1391 1393 False -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 False -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 False -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 False -gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed 2018-01-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 2230 329 347 1071 1071 362 362 492 492 64 64 2938 3793 755 773 False -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 False -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset 2022-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 False -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 False -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 False -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali 2020-03-30 nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 False -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation 2018-04-24 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 377 400 17 17 0 0 0 0 0 0 0 0 377 400 17 17 False -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 False -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 False -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 2018-05-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8329 9363 3336 3828 8009 8009 3130 3130 1577 1577 344 344 17915 18949 6810 7302 False -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. To update https://github.com/sequencing/gvcftools Variant Analysis 2016-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 False -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy 2022-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 False -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 2018-07-22 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 False -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hess hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope To update Astronomy hess_astro_tool 2024-02-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0.0.2+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 False -hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard To update https://github.com/VariantEffect/hgvsParseR/tree/master Variant Analysis hgvsparser 2024-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6346 6346 2 2 0 0 0 0 0 0 0 0 6346 6346 2 2 False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 False -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk 2024-02-03 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 1.0.0 hictk 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 9 9 0 0 0 0 0 0 0 0 17 17 9 9 False -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup 2017-03-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 7 0 7 0 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 901 1020 160 184 440 440 111 111 0 0 0 0 1341 1460 271 295 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 False -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.8.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 False -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 False -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 False -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 False -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 False -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 False -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids 2020-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.45 omero-py 5.11.1 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 404 404 37 37 0 0 0 0 24 24 1 1 428 428 38 38 False -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 False -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 False -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 False -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 False -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 False -intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter To update https://github.com/intermine Convert Formats intermine_galaxy_exchange 2018-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 6 12 72 87 13 15 108 108 1 1 217 241 20 28 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 False -intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20472 349984 2351 3007 45587 778988 4359 14116 6087 7417 484 561 72146 1136389 7194 17684 False -interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf 2020-07-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.13.0 Sequence analysis 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 107 7 10 758 19538 87 1246 16 24 2 2 806 19669 96 1258 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 False -irissv irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.21 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 False -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -jasminesv jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 9 9 53 53 19 19 0 0 0 0 85 85 28 28 False -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 False -jbrowse jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container 2016-11-08 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 False -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15624 330820 1864 2438 52317 513688 10198 39421 1329 1645 213 289 69270 846153 12275 42148 False -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id Text Manipulation join_files_by_id 2017-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy 2017-11-26 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1980 2697 345 410 0 0 0 0 1081 1081 44 44 3061 3778 389 454 False -jq jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 660 2374 61 63 336 336 82 82 281 281 11 11 1277 2991 154 156 False -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff 2017-09-27 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip 2018-05-16 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit 2021-02-11 iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7179 7179 509 509 11138 11138 1145 1145 0 0 0 0 18317 18317 1654 1654 False -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 False -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 False -kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers kegalign 2024-08-29 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 0.1.2.7 kegalign-full 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 5 5 1 1 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -king king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king 2021-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 False -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.4.14 kma 1.4.15 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 False -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 False -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 False -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 False -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 False -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 False -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 False -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 False -lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz 2018-02-19 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 Sequence alignment, Read mapping Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 77409 84356 447 475 156658 193590 870 3511 38579 38780 173 203 272646 316726 1490 4189 False -lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 3 4 0 0 0 0 8 10 5 5 15 19 8 9 False -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 False -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie 2022-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 False -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis 2019-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 5 5 5 4 5 5 5 4 0 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4176367 4176367 4301 4301 509615 509615 8213 8213 106342 106342 1815 1815 4792324 4792324 14329 14329 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 False -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 False -ltq_iquant_cli To update ltq_iquant_cli 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove 2020-07-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv 2020-11-12 iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1534 1534 199 199 0 0 0 0 0 0 0 0 1534 1534 199 199 False -lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 1.3 lumpy-sv 0.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 False -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 False -maf_stats maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats 2020-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 15 21 7 9 227 2470 52 464 1 1 1 1 243 2492 60 474 False -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 False -maftoaxt maftoaxt Convert dataset from MAF to axt format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_maftoaxt 2024-07-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt 469 ucsc-maftoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing 2018-03-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 Genetic variation analysis Genetics, Genetic variation, Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 11761 12093 873 889 5762 5762 473 473 5610 5610 343 343 23133 23465 1689 1705 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 False -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 False -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run 2021-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 9 9 0 0 0 0 0 0 0 0 24 24 9 9 False -manta manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta 2023-06-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 218 218 34 34 0 0 0 0 0 0 0 0 218 218 34 34 False -map_param_value map_param_value Map a parameter value to another value To update Text Manipulation map_param_value 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3780 3780 67 67 1012 1012 57 57 105 105 3 3 4897 4897 127 127 False -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 False -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer 2023-12-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 0 0 0 0 0 0 0 0 8 8 2 2 False -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 False -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 False -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 743 816 103 141 292 2868 82 459 0 0 0 0 1035 3684 185 600 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 False -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme 2018-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.5.6 meme 5.5.7 Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability 3 0 4 0 3 0 4 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 20990 22979 762 892 10975 25929 1551 3249 0 0 0 0 31965 48908 2313 4141 False -meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip 2018-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6413 7000 705 743 7260 7260 1171 1171 0 0 0 0 13673 14260 1876 1914 False -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco 2018-06-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 565922 566630 418 441 45844 107523 671 4353 19828 19994 100 137 631594 694147 1189 4931 False -merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 20905 31051 1906 2128 21780 132833 885 3172 1524 1925 122 152 44209 165809 2913 5452 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin 2020-04-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 Haplotype mapping GWAS study, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 False -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 False -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 False -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 False -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 False -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 False -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 False -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 False -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit 2016-12-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -mgf_formatter mgf_formatter Up-to-date mgf_formatter 2014-09-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 False -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 False -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 False -mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 8 8 17 63 6 19 0 0 0 0 26 74 14 27 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 2018-08-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 Pairwise sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 346530 349075 4323 4419 108535 108535 4075 4075 22331 22331 1166 1166 477396 479941 9564 9660 False -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 False -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 False -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 False -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko 2018-04-12 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 False -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 False -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 False -moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs 2019-07-28 iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 339 339 56 56 0 0 0 0 0 0 0 0 339 339 56 56 False -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 False -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mosdepth mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth 2022-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1278 1278 87 87 168 168 24 24 102 102 5 5 1548 1548 116 116 False -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 False -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 False -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 False -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 False -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 False -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 False -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps 2017-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 485 871 159 298 0 0 0 0 485 871 159 298 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 False -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 False -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 False -mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 49 5 5 81 417 23 118 0 0 0 0 125 466 28 123 False -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns 2020-10-19 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 False -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 False -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish 2018-06-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 9284 9694 215 229 0 0 0 0 2358 2358 49 49 11642 12052 264 278 False -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 False -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 False -ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download 2019-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6873 6873 1664 1664 17651 17651 4513 4513 6228 6228 972 972 30752 30752 7149 7149 False -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 False -ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.20.0 ncbi-datasets-cli Data handling, Sequence database search, Data retrieval Biological databases 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4417 4417 1024 1024 6940 6940 2275 2275 1 1 1 1 11358 11358 3300 3300 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct 2022-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 22.4 entrez-direct 22.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 3 0 2 False -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils 2020-08-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 4 0 0 4 0 0 0 2 0 0 0 0 0 0 0 7 7 0 2794 3191 533 664 0 0 0 0 0 0 0 0 2794 3191 533 664 False -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 False -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr 2022-08-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 6 6 0 0 0 0 0 0 0 0 12 12 6 6 False -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 False -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr 2020-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1403 1403 49 49 0 0 0 0 0 0 0 0 1403 1403 49 49 False -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM 2015-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24611 29662 633 716 15523 21395 740 1128 7751 8972 125 145 47885 60029 1498 1989 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 False -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ococo ococo Variant detection of SNVs To update https://github.com/karel-brinda/ococo Variant Analysis ococo 2017-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1850 1963 79 93 1370 1370 194 194 0 0 0 0 3220 3333 273 287 False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit 2017-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 582 663 68 69 0 0 0 0 0 0 0 0 582 663 68 69 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 False -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 False -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe 2022-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 False -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader Data Source packaged_annotation_loader 2022-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 False -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp 2022-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 Variant calling Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 2022-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.14.99 pbmm2 1.14.99 Pairwise sequence alignment, Sorting Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 17 17 0 0 0 0 0 0 0 0 70 70 17 17 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram 2016-06-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.2 openjdk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5505 5505 510 510 7932 8582 811 909 736 736 119 119 14173 14823 1440 1538 False -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 False -peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla 2024-02-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 False -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 False -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 False -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 False -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 False -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 False -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools 2017-09-28 bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat 2022-01-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 109 109 29 29 250 250 84 84 0 0 0 0 359 359 113 113 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 False -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard 2019-05-30 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.3.0 Formatting Sequencing 31 31 31 31 31 31 31 31 0 0 0 0 0 0 0 0 31 4 31 0 0 31 0 0 0 31 0 0 0 0 0 0 31 31 31 0 386934 399039 11024 11956 366646 589980 32000 57111 56622 62258 2845 3398 810202 1051277 45869 72465 False -pick_value pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value 2023-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1607 1607 41 41 490 490 53 53 127 127 4 4 2224 2224 98 98 False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 False -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 False -pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval 2015-03-06 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 613 640 48 54 1381 7804 201 1552 756 815 22 30 2750 9259 271 1636 False -pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3639 3774 414 461 9754 52522 1247 4531 1893 2433 191 318 15286 58729 1852 5310 False -pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update https://github.com/broadinstitute/pilon/wiki Variant Analysis pilon 2016-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 Sequence assembly, Analysis Assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9045 9458 1115 1144 7989 7989 1070 1070 3945 4137 726 741 20979 21584 2911 2955 False -pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel 2021-09-29 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign 2019-08-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1245 1245 231 231 9046 9046 630 630 0 0 0 0 10291 10291 861 861 False -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 False -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 False -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 False -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink 2020-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 Genetic variation analysis GWAS study 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 851 851 127 127 249 249 43 43 0 0 0 0 1100 1100 170 170 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 False -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 False -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat 2020-03-24 nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment 2016-11-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment 2016-11-07 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 False -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 False -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 False -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 False -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 False -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 False -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 False -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 False -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 False -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 False -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 False -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 False -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 False -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 False -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 False -protxml_to_xls protxml_to_xls To update protxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_eval psm_eval To update psm_eval 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 False -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2716 2716 104 104 134 134 43 43 40 40 1 1 2890 2890 148 148 False -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 False -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -pyvo_integration astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy To update Data Source astronomicalarchivestool 2023-08-26 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0.10.0 astropy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 6 6 0 0 0 0 0 0 0 0 53 53 6 6 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 False -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 False -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 False -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 False -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 False -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 False -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -query query Execute an SQL statement on a set of tables To update Text Manipulation query 2020-12-09 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -query_impc query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc 2023-10-11 iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular Text Manipulation 2017-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.1 python 3 3 3 1 3 3 3 1 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 130124 135361 1265 1305 11135 11135 922 922 5939 5939 153 153 147198 152435 2340 2380 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 False -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 False -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 False -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 False -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 False -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 False -regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace 2017-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 78648 78834 1144 1156 18063 18063 870 870 4455 6051 194 289 101166 102948 2208 2315 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 148572 169964 3525 3682 36694 113826 3910 8163 9713 10577 1475 1598 194979 294367 8910 13443 False -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 False -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file 2017-02-24 bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 577184 577312 463 492 43900 44233 283 373 2190 2190 112 112 623274 623735 858 977 False -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names 2017-05-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 514 573 69 83 0 0 0 0 0 0 0 0 514 573 69 83 False -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 415 721 128 219 0 0 0 0 415 721 128 219 False -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3543 3619 108 111 536 536 157 157 0 0 0 0 4079 4155 265 268 False -resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window 2016-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 86 8 9 138 216 30 57 0 0 0 0 213 302 38 66 False -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam 2019-04-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.21 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 11 11 520 520 31 31 0 0 0 0 560 560 42 42 False -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 False -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 False -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 False -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 False -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 False -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 False -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 False -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 False -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor 2023-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths 2022-10-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign 2022-03-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba 2022-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools 2022-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser 2022-06-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps 2016-01-29 earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 False -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1155 1251 57 63 2264 18187 189 1748 525 590 10 17 3944 20028 256 1828 False -sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python 1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 278 12 26 3554 76029 450 6346 229 345 16 29 3879 76652 478 6401 False -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba 2020-05-19 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 684 684 17 17 684 684 17 17 False -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! Up-to-date https://github.com/biod/sambamba SAM sambamba 2016-06-23 bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 1.0.1 sambamba 1.0.1 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 297 297 51 51 0 0 0 0 0 0 0 0 297 297 51 51 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools To update https://github.com/samtools/samtools SAM 2021-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.20 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa 2020-12-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.2 sansa 0.2.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 138 138 36 36 0 0 0 0 0 0 0 0 138 138 36 36 False -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 False -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 False -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol 2022-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scaffold scaffold, scaffold_export To update scaffold 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 False -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -scripting singularity_scriptrunner suite_scripting To update https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ Text Manipulation scripting tools 2023-07-29 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr 2020-02-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5106 5106 116 116 6419 6419 241 241 0 0 0 0 11525 11525 357 357 False -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 281 2284 10 53 0 0 0 0 0 0 0 0 281 2284 10 53 False -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign 2024-04-18 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.7 segalign-galaxy 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 252 252 47 47 0 0 0 0 252 252 47 47 False -segemehl segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1095 1306 98 113 0 0 0 0 0 0 0 0 1095 1306 98 113 False -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 False -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 False -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 False -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 False -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 False -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sgwb sgwb_astro_tool SGWB To update Astronomy sgwb_astro_tool 2024-04-17 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0.0.1+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 0 0 0 0 0 0 0 0 5 5 2 2 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 64 4 4 0 0 0 0 0 0 0 0 54 64 4 4 False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 27232 36366 2184 2789 16648 84460 4191 18767 2785 3276 373 452 46665 124102 6748 22008 False -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1620 2660 378 589 10551 24579 682 1851 284 398 67 83 12455 27637 1127 2523 False -sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 276 379 30 42 972 9053 146 1008 644 689 5 7 1892 10121 181 1057 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext 2021-02-28 iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 0 2 4 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 220 220 68 68 0 0 0 0 416 416 10 10 636 636 78 78 False -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 False -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 False -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes 2019-04-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 False -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 False -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 False -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists 2019-10-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6555 6555 807 807 5336 5336 171 171 1143 1143 182 182 13034 13034 1160 1160 False -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites 2017-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6597 6597 663 663 1467 1467 256 256 1279 1279 114 114 9343 9343 1033 1033 False -snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff 2018-07-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 5 5 5 5 5 5 5 5 0 0 0 0 0 1 0 0 0 5 5 0 0 5 0 0 0 5 0 0 0 0 0 0 5 5 5 0 103826 108296 7181 7908 115727 178110 15871 22769 11817 13155 2148 2321 231370 299561 25200 32998 False -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 SNP detection DNA polymorphism, Nucleic acid sites, features and motifs 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 764895 764895 1276 1276 94572 94572 1636 1636 26990 26990 561 561 886457 886457 3473 3473 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region To update https://github.com/BrownfieldPlantLab/SNPFreqPlot Variant Analysis snpfreqplot 2020-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 3683 3683 338 338 1401 1401 433 433 1029 1029 95 95 6113 6113 866 866 False -snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift 2015-04-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 8 8 8 8 8 8 8 8 0 0 0 0 0 8 0 0 0 0 8 0 0 8 0 0 0 8 0 0 0 0 0 0 8 8 8 0 5142904 5146618 3602 4283 382391 421190 7013 9678 104030 105024 960 1184 5629325 5672832 11575 15145 False -snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 52 55 23 24 421 421 75 75 0 0 0 0 473 476 98 99 False -snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 509 554 107 128 474 474 190 190 0 0 0 0 983 1028 297 318 False -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv 2021-03-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 False -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_file_on_column tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5995 6261 408 453 2150 2150 311 311 26 26 2 2 8171 8437 721 766 False -split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection 2019-08-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16415 16623 968 984 9133 9133 672 672 4140 4140 148 148 29688 29896 1788 1804 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta 2015-10-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1772 1811 278 294 3012 3012 564 564 0 0 0 0 4784 4823 842 858 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 False -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 False -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 False -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 False -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign 2022-10-02 iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka 2021-01-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 669 669 112 112 1261 1261 417 417 0 0 0 0 1930 1930 529 529 False -stress_ng stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng 2021-03-04 bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 3 3 0 0 0 0 0 0 0 0 62 62 3 3 False -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 False -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 False -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 False -subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 566512 567199 410 470 49985 184650 1473 7631 20648 20897 155 188 637145 772746 2038 8289 False -subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1178 1450 124 141 3169 40539 636 3435 799 950 26 38 5146 42939 786 3614 False -suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 249 249 32 32 16 16 10 10 102 102 16 16 367 367 58 58 False -suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 False -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib 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qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 False -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 False -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 False -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 False -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 False -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 False -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 False -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 False -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 False -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink 2017-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 False -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 False -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar 2013-12-02 devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16526 64515 2803 7456 0 0 0 0 16526 64515 2803 7456 False -table_compute table_compute Perform general-purpose table operations To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute Text Manipulation table_compute 2019-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 216072 216115 1811 1814 12326 12326 1558 1558 16136 16136 256 256 244534 244577 3625 3628 False -tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2188 2220 33 38 0 0 0 0 0 0 0 0 2188 2220 33 38 False -tabular_to_fasta tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 329032 333057 1489 1702 79033 215770 2441 8587 27876 33727 296 360 435941 582554 4226 10649 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 False -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 False -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 False -tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter 2019-10-03 iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22977 22977 461 461 3888 3888 274 274 3611 3611 80 80 30476 30476 815 815 False -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 False -tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.1 tbvcfreport 1.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2955 2955 335 335 6090 6090 348 348 2347 2347 72 72 11392 11392 755 755 False -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 False -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 False -text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing 2019-01-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 20 20 20 20 20 20 20 20 0 0 0 0 0 0 0 0 19 1 19 0 0 19 0 0 0 20 0 0 0 0 0 0 19 19 19 0 3898014 4015573 37698 42095 648268 915282 47636 69828 103365 105214 7778 7953 4649647 5036069 93112 119876 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 False -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 False -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 False -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 False -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 False -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 False -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update 2021-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.8 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 3314 3314 124 124 0 0 0 0 0 0 0 0 3314 3314 124 124 False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 False -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 False -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 False -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler 2019-04-15 nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmer trimmer Trim leading or trailing characters. To update Text Manipulation trimmer 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 5304 7438 447 512 15698 108672 658 2946 266 822 53 81 21268 116932 1158 3539 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 False -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services 2018-06-20 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 255 379 31 37 281 281 64 64 0 0 0 0 536 660 95 101 False -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa 2016-08-19 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 469 ucsc-twobittofa 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 413 511 84 118 441 441 123 123 21 21 2 2 875 973 209 243 False -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 False -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 False -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_axttomaf 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf 469 ucsc-axttomaf 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 False -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_nettoaxt 2024-09-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt 469 ucsc-nettoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 False -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 False -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 False -unzip unzip Unzip file To update https://github.com/bmcv Convert Formats unzip 2019-08-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 6.0 unzip 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6942 7024 1345 1356 1 1 1 1 2461 2461 266 266 9404 9486 1612 1623 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 False -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 False -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java 2020-08-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 381 381 37 37 0 0 0 0 0 0 0 0 381 381 37 37 False -variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer 2019-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 95 95 14 14 516 516 67 67 0 0 0 0 611 611 81 81 False -varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan 2018-11-29 iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 10711 11502 1442 1560 16705 16705 3135 3135 1036 1036 100 100 28452 29243 4677 4795 False -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf 2022-11-28 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 2013-11-17 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5058 6139 606 699 17232 53268 2965 5686 2298 2656 424 482 24588 62063 3995 6867 False -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 False -vcf2maf vcf2maf vcf2maf: Convert VCF into MAF To update https://github.com/mskcc/vcf2maf Convert Formats vcf2maf 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1097 1097 46 46 0 0 0 0 65 65 5 5 1162 1162 51 51 False -vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 221 57 65 1399 2700 209 584 0 0 0 0 1590 2921 266 649 False -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 169090 169679 823 874 16304 42215 1141 2594 2485 2511 169 172 187879 214405 2133 3640 False -vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 263 340 31 54 263 342 31 56 False -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 513 569 6 9 513 569 6 9 False -vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 400 455 129 140 0 0 0 0 238 606 19 56 638 1061 148 196 False -vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 3 0 0 0 0 335 463 19 28 335 482 19 31 False -vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 882 888 30 32 6118 8261 36 114 175 184 6 6 7175 9333 72 152 False -vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6879 17157 897 1219 7585 14509 1245 1925 1648 1681 225 229 16112 33347 2367 3373 False -vcfanno vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 SNP annotation Genetic variation, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1139 1139 174 174 0 0 0 0 0 0 0 0 1139 1139 174 174 False -vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2797 2850 157 181 3668 14532 652 1392 494 507 61 63 6959 17889 870 1636 False -vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 203 62 66 497 1828 155 387 184 197 11 11 870 2228 228 464 False -vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3017 4049 185 210 4709 20250 406 1147 507 527 40 42 8233 24826 631 1399 False -vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 416 478 35 40 3969 10457 82 309 362 378 8 8 4747 11313 125 357 False -vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 767 96 106 803 1895 222 627 241 256 16 17 1789 2918 334 750 False -vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1422 2020 284 505 4951 19530 1021 2669 493 516 60 62 6866 22066 1365 3236 False -vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 233 253 37 42 234 1839 79 287 199 214 11 12 666 2306 127 341 False -vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 572 585 90 92 2063 2427 139 296 272 290 19 22 2907 3302 248 410 False -vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37489 47142 2113 2218 75128 162296 5730 10533 2626 2736 320 331 115243 212174 8163 13082 False -vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 926 957 155 173 2291 5323 313 985 251 265 28 31 3468 6545 496 1189 False -vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 172 183 21 25 351 879 67 201 312 342 15 16 835 1404 103 242 False -vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 778 794 107 112 2414 3721 179 508 209 225 20 21 3401 4740 306 641 False -vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 502 555 134 143 3428 6338 266 858 220 235 23 24 4150 7128 423 1025 False -vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1964 1991 182 186 1937 3846 188 644 567 601 26 27 4468 6438 396 857 False -vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 269 310 38 42 358 1071 89 287 179 213 12 14 806 1594 139 343 False -vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 711 28 33 403 831 75 200 190 214 10 12 1183 1756 113 245 False -vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 168 13 15 153 350 27 75 184 192 6 6 498 710 46 96 False -vcfselectsamples vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 830 900 69 88 1315 6257 237 959 344 363 20 21 2489 7520 326 1068 False -vcfsort vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1868 1904 174 185 18378 24175 422 1279 537 674 70 73 20783 26753 666 1537 False -vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 192 81 90 1853 3943 581 1280 144 156 13 16 2152 4291 675 1386 False -vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 440 594 127 142 0 0 0 0 0 16 0 12 440 610 127 154 False -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus 2016-10-16 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcftools_isec vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 537 104 118 0 1 0 1 39 496 28 48 418 1034 132 167 False -vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 817 1084 244 273 0 0 0 0 93 448 44 60 910 1532 288 333 False -vcftools_slice vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 423 56 60 6261 8115 133 362 127 157 10 19 6798 8695 199 441 False -vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 142 46 49 0 0 0 0 120 142 12 19 254 284 58 68 False -vcfvcfintersect vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 976544 977015 703 748 64155 81830 981 2103 11044 11069 225 229 1051743 1069914 1909 3080 False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 False -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 False -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 False -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -weblogo3 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 2017-11-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2720 2818 206 228 10299 30578 1354 3657 1226 1285 50 59 14245 34681 1610 3944 False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 False -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig 2024-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 469 ucsc-wigtobigwig 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1601 1601 106 106 1108 1108 172 172 200 200 15 15 2909 2909 293 293 False -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 False -winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap 2021-04-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 279 279 46 46 12 12 4 4 0 0 0 0 291 291 50 50 False -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 False -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 False -xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet 2021-10-18 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 17 17 0 0 0 0 0 0 0 0 59 59 17 17 False -xpath xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 235 7 8 0 1 0 1 0 0 0 0 128 236 7 9 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 False -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 False -zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 96 9 12 0 0 0 0 0 0 0 0 83 96 9 12 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False diff --git a/communities/proteomics/resources/tools_filtered_by_ts_categories.json b/communities/proteomics/resources/tools_filtered_by_ts_categories.json new file mode 100644 index 00000000..4316975f --- /dev/null +++ b/communities/proteomics/resources/tools_filtered_by_ts_categories.json @@ -0,0 +1,8536 @@ +[ + { + "Galaxy wrapper id": "peptimapper", + "Galaxy tool ids": [ + "peptimapper_clustqualify", + "peptimapper_clust_to_gff", + "peptimapper_pep_match", + "peptimapper_pep_novo_tag" + ], + "Description": "Proteogenomics workflow for the expert annotation of eukaryotic genomes", + "bio.tool id": null, 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq 2022-05-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 307 307 80 80 8 8 3 3 3 3 1 1 318 318 84 84 False -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 1739 7051 131 133 False -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1156 13842 40 42 0 0 0 0 121 121 4 4 1277 13963 44 46 False -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features 0.0.1-4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 591 6863 38 40 0 0 0 0 119 119 3 3 710 6982 41 43 False -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_histogram_equalization 2019-07-23 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization 0.18.1 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 762 782 100 101 0 0 0 0 230 230 14 14 992 1012 114 115 False -2d_simple_filter ip_filter_standard 2d simple filter scipy To update https://github.com/bmcv Imaging 2d_simple_filter 2019-01-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter 1.12.0 scipy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 948 6261 98 100 0 0 0 0 153 153 13 13 1101 6414 111 113 False -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments 2018-10-24 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 119 14 17 0 0 0 0 0 0 0 0 45 119 14 17 False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster 2018-10-22 rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 189 3094 23 25 0 0 0 0 0 0 0 0 189 3094 23 25 False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25532 50045 45 57 0 0 0 0 0 0 0 0 25532 50045 45 57 False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing 2017-01-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1119 2115 50 62 0 0 0 0 0 0 0 0 1119 2115 50 62 False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align 2018-10-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 37 108 1 3 0 0 0 0 0 0 0 0 37 108 1 3 False -EMLassemblyline annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline 2023-12-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.0+galaxy0 r-base 0 0 11 9 0 0 11 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 516 516 128 128 0 0 0 0 0 0 0 0 516 516 128 128 False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization 2023-10-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base 0 0 6 5 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 352 352 36 36 0 0 0 0 0 0 0 0 352 352 36 36 False -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source 2015-11-17 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 474 2914 132 163 0 0 0 0 0 0 0 0 474 2914 132 163 False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa 2016-12-15 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 47 6 6 0 0 0 0 0 0 0 0 40 47 6 6 False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 80 150 18 23 0 0 0 0 0 0 0 0 80 150 18 23 False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) 2023-11-10 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 53 18 18 0 0 0 0 0 0 0 0 53 53 18 18 False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25572 50177 45 57 0 0 0 0 0 0 0 0 25572 50177 45 57 False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 3210 62854 96 124 0 0 0 0 0 0 0 0 3210 62854 96 124 False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa 2020-11-13 ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 1038 1038 146 146 0 0 0 0 849 849 38 38 1887 1887 184 184 False -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot 2017-02-22 rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 71 9 10 0 0 0 0 0 0 0 0 45 71 9 10 False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna 2016-12-15 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1202 2121 48 62 0 0 0 0 0 0 0 0 1202 2121 48 62 False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing 2017-01-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1116 1897 57 71 0 0 0 0 0 0 0 0 1116 1897 57 71 False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan 2017-05-18 rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 991 3060 50 62 0 0 0 0 0 0 0 0 991 3060 50 62 False -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter 2019-08-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2467 2959 88 124 0 0 0 0 1097 1097 18 18 3564 4056 106 142 False -TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1003 1022 48 52 0 0 0 0 0 0 0 0 1003 1022 48 52 False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns 2021-01-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 20 20 0 0 0 0 0 0 0 0 43 43 20 20 False -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq 2021-10-08 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 49465 49465 281 281 0 0 0 0 0 0 0 0 49465 49465 281 281 False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas 2019-11-20 nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate 2017-07-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 Antimicrobial resistance prediction Genomics, Microbiology 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 619817 622353 4097 4130 320454 320454 2915 2915 496156 503743 2012 2227 1436427 1446550 9024 9272 False -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr 2023-04-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.19 abritamr 1.0.19 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 1139 1139 109 109 False -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.9 abyss 2.3.9 Genome assembly, De-novo assembly, Scaffolding Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5543 5543 1042 1042 1301 1305 413 414 2030 2030 299 299 8874 8878 1754 1755 False -adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.4 adapterremoval 2.3.4 Sequence trimming, Sequence merging, Primer removal 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 348 348 62 62 0 0 0 0 0 0 0 0 348 348 62 62 False -add_input_name_as_column addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column 2020-03-24 mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 76834 86002 227 246 20174 20953 312 395 11 11 2 2 97019 106966 541 643 False -add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file 2020-11-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 15933 15933 378 378 1736 1736 214 214 380 380 28 28 18049 18049 620 620 False -add_value addValue Add a value as a new column. To update Text Manipulation add_value 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 37860 374587 1293 1610 17588 293713 1243 6197 3873 4397 202 229 59321 672697 2738 8036 False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 False -agat agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat 2023-05-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.4.0 agat 1.4.1 Data handling, Genome annotation Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 244 244 0 0 0 0 119 119 10 10 1555 1555 254 254 False -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 262 262 36 36 False -align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 511 541 32 35 0 0 0 0 0 0 0 0 511 541 32 35 False -allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro 2017-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools 2020-04-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools 7 2 7 0 7 2 7 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 41793 41881 510 511 1126 1126 159 159 1552 1552 85 85 44471 44559 754 755 False -amplican amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican 2021-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 Alignment, Standardisation and normalisation PCR experiment, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 17 17 0 0 0 0 0 0 0 0 81 81 17 17 False -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 2022-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.9 Analysis, Visualisation Biodiversity 0 0 19 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1213 1213 155 155 0 0 0 0 0 0 0 0 1213 1213 155 155 False -amrfinderplus amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus 2023-05-12 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5734 5734 334 334 1035 1035 106 106 0 0 0 0 6769 6769 440 440 False -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc 2022-07-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 DNA barcoding Microbial ecology, Metagenomics, Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 7 7 0 0 0 0 0 0 0 0 26 26 7 7 False -anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion Up-to-date https://github.com/bmcv Imaging anisotropic_diffusion 2018-12-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0.4.0 medpy 0.4.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 41 2 2 0 0 0 0 0 0 0 0 36 41 2 2 False -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids 2018-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Annotation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 29266 30655 2849 2973 59299 66180 5917 6355 5644 5644 1049 1049 94209 102479 9815 10377 False -antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna 2015-04-30 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 292 306 5 7 0 0 0 0 0 0 0 0 292 306 5 7 False -antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash 2015-02-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15949 16490 726 811 5113 5113 649 649 6043 6043 169 169 27105 27646 1544 1629 False -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 5 5 5 False -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services 2020-06-29 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 3600 3760 883 911 6 6 4 4 0 0 0 0 3606 3766 887 915 False -appendfdr append_fdr To update appendfdr 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-14 ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 9 9 0 0 0 0 0 0 0 0 75 75 9 9 False -aquainfra_ogc_api_processes aquainfra_ogc_api_processes Wrapper for OGC API Processes developed in the AquaINFRA project. To update https://github.com/AquaINFRA/galaxy Ecology 2024-10-10 ecology https://github.com/AquaINFRA/tools-ecology/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -aresite2 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 2017-02-01 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 59 74 10 12 0 0 0 0 0 0 0 0 59 74 10 12 False -argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. Gene functional annotation Up-to-date https://github.com/BigDataBiology/argNorm Genome annotation argnorm 2024-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm 0.6.0 argnorm 0.6.0 Gene functional annotation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ Sequence Analysis, Data Source art 2015-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 Conversion Bioinformatics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 140 140 9 9 0 0 0 0 0 0 0 0 140 140 9 9 False -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning 2020-10-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis 2020-04-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 Sequence alignment Genomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 9021 9021 238 238 0 0 0 0 0 0 0 0 9021 9021 238 238 False -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services 2017-08-11 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats 2023-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees Up-to-date https://github.com/smirarab/ASTRAL Phylogenetics astral 2024-08-28 iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 5.7.8 astral-tree 5.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 151 151 5 5 151 151 5 5 False -astropytools astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo AstropyTools library contains Galaxy tools for elementary Astrophysical operations To update https://github.com/astropy/astropy Astronomy astropytools 2023-04-11 volodymyrss https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools 0.1.0+galaxy0 astropy 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 5 5 0 0 0 0 0 0 0 0 13 13 5 5 False -atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters 2018-06-20 rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 279 62 72 0 0 0 0 0 0 0 0 232 279 62 72 False -augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10109 11052 1378 1509 12573 12573 2206 2206 5274 5274 369 369 27956 28899 3953 4084 False -augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus 2017-10-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12890 13988 1826 1988 14901 14901 2633 2633 6187 6187 511 511 33978 35076 4970 5132 False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology 2022-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.7 Protein disorder prediction, Protein secondary structure prediction 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 369 369 19 19 0 0 0 0 0 0 0 0 369 369 19 19 False -background_removal background_removal Background removal filters using scikit-image To update https://github.com/bmcv Imaging background_removal 2024-07-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0.24.0 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -bakta bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.4 bakta 1.9.4 Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11117 11117 534 534 19 19 1 1 9601 9601 167 167 20737 20737 702 702 False -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats 2017-10-13 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx 2015-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 131 15 20 329 785 50 210 0 0 0 0 412 916 65 230 False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper 2020-04-28 nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamhash bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 158 181 40 44 0 0 0 0 0 0 0 0 158 181 40 44 False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 14693 15620 653 721 61872 101400 1656 5678 39 39 3 3 76604 117059 2312 6402 False -bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter 2017-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115954 124795 2994 3180 95433 142254 6712 10660 5793 5793 497 497 217180 272842 10203 14337 False -bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM 2017-06-09 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 Data handling, Sequence alignment analysis Sequencing, Sequence analysis 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 9073 9073 401 401 2746 2746 224 224 103 103 10 10 11922 11922 635 635 False -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil 2021-03-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 20 20 69 69 21 21 258 258 1 1 372 372 42 42 False -bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 Sequence assembly visualisation Genomics, Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 55392 56095 4951 5035 47603 47603 4916 4916 18089 18089 3121 3121 121084 121787 12988 13072 False -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse 2016-06-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter 2019-02-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source 2022-03-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update https://github.com/tseemann/barrnap Sequence Analysis barrnap 2017-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 Gene prediction Genomics, Model organisms, Model organisms 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6041 6041 316 316 0 0 0 0 6723 7273 240 322 12764 13314 556 638 False -basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 226 308 27 35 2615 45557 302 2284 482 522 32 36 3323 46387 361 2355 False -baseline_calculator tt_baseline Toxicity prediction using QSAR models To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology, Text Manipulation baseline_toxicity_calculator 2024-03-25 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0.1.0+galaxy0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil 2019-05-22 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 306 311 82 83 467 467 99 99 0 0 0 0 773 778 181 182 False -batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers batched_lastz 2024-04-30 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 123 5 5 0 0 0 0 123 123 5 5 False -bax2bam bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam 2019-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208 208 26 26 210 210 30 30 0 0 0 0 418 418 56 56 False -bayescan BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan 2017-03-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 90 28 28 0 0 0 0 0 0 0 0 90 90 28 28 False -bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://www.encodeproject.org/software/bedgraphtobigwig/ Convert Formats bbgbigwig 2024-06-14 iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig 0.1 ucsc-bedgraphtobigwig 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 7 7 175 175 26 26 0 0 0 0 217 217 33 33 False -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq To update https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools 2021-10-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.08 bbmap 39.10 RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq 6 3 5 0 6 3 5 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 11989 11989 768 768 4458 4458 652 652 2507 2507 80 80 18954 18954 1500 1500 False -bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.21 Data handling, Variant calling DNA polymorphism, GWAS study, Genotyping experiment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 False -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 2023-08-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 33 33 9 9 0 0 0 0 0 0 0 0 33 33 9 9 False -beacon2-import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://pypi.org/project/beacon2-import/ Variant Analysis Beacon2_Import 2024-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import 2.2.4 beacon2-import 2.2.4 Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases 0 0 12 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 7 7 0 0 0 0 0 0 0 0 22 22 7 7 False -beagle beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle 2021-07-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 88 88 28 28 0 0 0 0 0 0 0 0 88 88 28 28 False -bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map 2018-01-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 419 134 137 363 363 99 99 158 158 13 13 931 940 246 249 False -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed 2023-08-08 iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 36 36 181 181 62 62 0 0 0 0 274 274 98 98 False -bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 Mapping Genomics 37 37 37 37 37 37 37 37 0 0 0 0 0 0 0 0 37 6 37 0 0 37 0 0 0 37 0 0 0 0 0 0 37 37 37 0 916111 962278 13235 14525 407944 647621 25849 41751 84008 89233 2486 2832 1408063 1699132 41570 59108 False -bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon 2021-05-28 iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1611 1611 262 262 763 763 67 67 543 543 30 30 2917 2917 359 359 False -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka 2019-03-08 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 617 617 63 63 617 617 63 63 False -best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 14 253 7 72 0 0 0 0 17 257 10 76 False -bfconvert ip_convertimage Convert image python-bioformats Up-to-date https://github.com/bmcv Imaging, Convert Formats bfconvert 2019-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert 6.7.0 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1635 1671 123 124 0 0 0 0 334 334 21 21 1969 2005 144 145 False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download 2023-12-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape 2024-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 544 544 20 20 0 0 0 0 0 0 0 0 544 544 20 20 False -bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files bigtools bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed Sequence Analysis bigwig_outlier_bed 2024-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed 0.2.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 218 218 5 5 0 0 0 0 0 0 0 0 218 218 5 5 False -bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph 2015-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph 2021-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 469 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5769 6802 567 650 0 0 0 0 0 3 0 1 5769 6805 567 651 False -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig 2018-09-25 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 469 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -binary2labelimage ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage 2017-02-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage 0.5 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 401 1385 87 88 0 0 0 0 188 188 9 9 589 1573 96 97 False -binaryimage2points ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points 0.1-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 29 1 1 0 0 0 0 0 0 0 0 24 29 1 1 False -binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 42 42 0 0 0 0 0 0 0 0 126 126 42 42 False -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d 2018-10-03 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 5 4 5 0 5 4 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 10600 10729 1150 1159 1042 1042 255 255 2756 2756 215 215 14398 14527 1620 1629 False -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers 2018-04-23 iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.9 python-bioext 0.21.9 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 17413 17413 822 822 15349 15349 2020 2020 2 2 1 1 32764 32764 2843 2843 False -bioformats2raw bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw 2023-11-02 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 61 4 4 0 0 0 0 0 0 0 0 61 61 4 4 False -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel 2018-08-01 nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter 2019-03-15 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -bioimaging bioimage_inference Load model from BioImage.IO and make inferences pytorch pytorch pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Machine learning, Computer science To update https://github.com/bgruening/galaxytools Imaging bioimage_inference 2024-08-02 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging 2.4.1 python Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 0 0 0 0 0 0 0 0 2 2 1 1 False -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe 2023-01-25 mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1137 1137 97 97 1029 1029 71 71 0 0 0 0 2166 2166 168 168 False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics 2016-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 Formatting Laboratory information management, Sequence analysis 2 2 6 0 2 2 6 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12725 12725 297 297 2851 5049 450 638 2171 2371 214 239 17747 20145 961 1174 False -biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels 2023-11-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 11 11 0 0 0 0 0 0 0 0 25 25 11 11 False -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn 2020-01-30 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 493 493 119 119 441 441 148 148 0 0 0 0 934 934 267 267 False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano 2021-05-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 151 151 143 143 43 43 596 596 22 22 1286 1286 216 216 False -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 2015-08-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 Data handling, Service invocation Genomics, Software engineering 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7738 7931 478 508 8301 8301 849 849 1369 1369 154 154 17408 17601 1481 1511 False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis 2020-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 Sequence analysis Mobile genetic elements, Workflows 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6243 6243 375 375 0 0 0 0 6243 6243 375 375 False -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer 2020-12-11 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot 2023-01-06 iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 1 1 0 0 0 0 0 0 0 0 3 3 1 1 False -bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark 2018-08-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 4 4 4 0 13715 14997 992 1099 0 0 0 0 197 197 22 22 13912 15194 1014 1121 False -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast 2022-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 738 738 151 151 0 0 0 0 2 2 1 1 740 740 152 152 False -blast2go blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go 2015-12-08 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1063 1237 257 300 0 0 0 0 0 0 0 0 1063 1237 257 300 False -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser 2015-08-06 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 417 438 99 104 0 0 0 0 0 0 0 0 417 438 99 104 False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp 2015-01-24 galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.16.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh 2016-12-05 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24916 27120 283 347 0 0 0 0 0 0 0 0 24916 27120 283 347 False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold 2016-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched 2017-10-03 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 1 1 0 0 0 0 8 8 1 1 False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 585 585 102 102 172 172 63 63 135 135 16 16 892 892 181 181 False -blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr 2015-05-21 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 264392 265217 483 552 0 0 0 0 0 0 0 0 264392 265217 483 552 False -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1527 1527 79 79 6 6 1 1 317 317 26 26 1850 1850 106 106 False -blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 768 3043 97 119 14 14 11 11 276 276 9 9 1058 3333 117 139 False -blockclust blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 811 1501 54 79 64 64 29 29 561 561 15 15 1436 2126 98 123 False -bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 2018-04-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 Read mapping Mapping, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 397893 427447 12133 13176 577209 903193 33086 52020 60105 67495 3779 4271 1035207 1398135 48998 69467 False -bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 24164 25149 1320 1480 17537 203397 1330 17491 15654 15992 291 351 57355 244538 2941 19322 False -bracken est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken 2019-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 3.0 bracken 3.0 Statistical calculation Metagenomics, Microbial ecology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 51378 51378 775 775 3298 3298 160 160 1660 1660 63 63 56336 56336 998 998 False -braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker 2021-10-05 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 165 165 48 48 0 0 0 0 0 0 0 0 165 165 48 48 False -braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 2023-07-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1938 1938 294 294 0 0 0 0 412 412 71 71 2350 2350 365 365 False -breseq breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq 2019-10-21 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.39.0 Polymorphism detection Sequencing, Sequence analysis, DNA mutation 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 2976 2976 98 98 0 0 0 0 884 884 70 70 3860 3860 168 168 False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics 2017-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1186 1356 21 32 0 0 0 0 0 0 0 0 1186 1356 21 32 False -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections 2015-11-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.58 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 1518 1526 73 76 1520 1528 74 77 False -busco busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco 2019-12-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.7.1 busco 5.8.0 Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 102717 103051 3877 3926 34251 34251 3506 3506 33192 34369 2439 2525 170160 171671 9822 9957 False -bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa 2017-11-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 2 976935 1017671 13526 14401 474702 681286 32627 47624 79802 87191 4219 4954 1531439 1786148 50372 66979 False -bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 2021-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 Sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 56619 56619 2324 2324 36631 36631 2808 2808 18121 18121 713 713 111371 111371 5845 5845 False -bwameth bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth 2016-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7970 11724 643 826 5524 5524 611 611 1242 1242 114 114 14736 18490 1368 1551 False -c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s 2021-04-13 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.3.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 234 234 11 11 4 4 4 4 92 92 3 3 330 330 18 18 False -cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus 2023-01-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 Multiple sequence alignment, Genome alignment Genomics, Sequence assembly, Mapping, Phylogenetics 0 2 2 1 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 299 299 61 61 0 0 0 0 1339 1339 95 95 1638 1638 156 156 False -cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads 2021-06-19 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 52 52 1 1 0 0 0 0 0 0 0 0 52 52 1 1 False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param 2021-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1393 1393 10 10 0 0 0 0 0 0 0 0 1393 1393 10 10 False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp 2023-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera 2023-05-25 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 677 787 114 120 60 60 30 30 734 746 26 26 1471 1593 170 176 False -cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber 2024-05-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.7 cami-amber 2.0.7 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 195 195 4 4 0 0 0 0 0 0 0 0 195 195 4 4 False -canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 66 75 16 18 141 505 31 147 0 0 0 0 207 580 47 165 False -canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu 2018-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 De-novo assembly Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13360 14618 1383 1444 0 0 0 0 3542 3542 385 385 16902 18160 1768 1829 False -cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 9869 9869 158 158 0 0 0 0 6886 6886 146 146 16755 16755 304 304 False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets Up-to-date http://cardinalmsi.org Proteomics, Metabolomics 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 3.4.3 bioconductor-cardinal 3.4.3 0 9 11 11 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 9 11 9 0 41875 50702 663 713 12 12 1 1 7512 7512 231 231 49399 58226 895 945 False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool 2019-11-27 iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly 5 2 5 0 5 2 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3835 3835 597 597 1359 1359 467 467 646 646 98 98 5840 5840 1162 1162 False -categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 41 4 5 0 0 0 0 168 186 12 14 205 227 16 19 False -ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 175 28 39 0 0 0 0 0 0 0 0 88 175 28 39 False -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup 2015-04-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5946 7379 407 628 0 0 0 0 5946 7379 407 628 False -cdhit cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit 2018-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 Sequence clustering Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10414 10414 510 510 2 2 1 1 2 2 1 1 10418 10418 512 512 False -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis 2021-09-01 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 218 218 17 17 0 0 0 0 0 0 0 0 218 218 17 17 False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.10 cellpose 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 4 4 0 0 0 0 0 0 0 0 14 14 4 4 False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler 2020-05-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype 0 23 23 19 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 4773 4773 749 749 0 0 0 0 5688 5688 94 94 10461 10461 843 843 False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update https://github.com/CellProfiler/CellProfiler Imaging cellprofiler4 2021-09-15 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.7 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55 55 11 11 0 0 0 0 0 0 0 0 55 55 11 11 False -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 False -cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm 2021-06-15 climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 2 2 0 0 0 0 0 0 0 0 14 14 2 2 False -cfm cfmid Competitive Fragmentation Modeling (CFM) Up-to-date https://sourceforge.net/p/cfm-id/ Metabolomics cfmid 2019-03-07 computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 33 cfm 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services 2018-11-05 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology 2023-03-06 ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 183 183 20 20 0 0 0 0 0 0 0 0 183 183 20 20 False -change_case ChangeCase Convert column case. To update Text Manipulation change_case 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 10606 12531 2204 2547 9044 17167 1748 2394 923 938 240 245 20573 30636 4192 5186 False -charts charts Enables advanced visualization options in Galaxy Charts To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ Visualization charts 2018-01-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3383 4001 1576 1822 7870 13727 3823 6880 249 350 108 145 11502 18078 5507 8847 False -chatgpt chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt Machine Learning chatgpt_openai_api 2024-08-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 12 12 0 0 0 0 0 0 0 0 62 62 12 12 False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Up-to-date https://github.com/Ecogenomics/CheckM Metagenomics checkm 2022-07-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.3 checkm-genome 1.2.3 Sequence assembly validation, Sequence composition calculation, Statistical calculation Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 7500 7500 930 930 0 0 0 0 0 0 0 0 7500 7500 930 930 False -checkv checkv_end_to_end Assess quality of single-contig viral genomes checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Up-to-date https://bitbucket.org/berkeleylab/checkv/ Metagenomics checkv 2024-09-13 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv 1.0.3 checkv 1.0.3 Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 False -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca 2024-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.10 0 0 8 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 727 727 76 76 0 0 0 0 0 0 0 0 727 727 76 76 False -chipseeker chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker 2018-05-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 16468 18344 956 991 33692 34453 2559 2625 2948 2948 104 104 53108 55745 3619 3720 False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 False -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.9.post1 chopin2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 6 6 0 0 0 0 14 14 6 6 False -chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister 2020-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2696 2696 398 398 0 0 0 0 1235 1235 186 186 3931 3931 584 584 False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer 2016-06-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 263 32 40 0 0 0 0 209 209 6 6 420 472 38 46 False -circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 2022-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 RNA splicing, Gene transcripts, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 524 524 32 32 0 0 0 0 0 0 0 0 524 524 32 32 False -circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos 2020-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 Sequence visualisation 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 26265 26265 2483 2483 31332 31332 3535 3535 26359 26359 999 999 83956 83956 7017 7017 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 2022-06-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 1.0.8 clair3 1.0.10 Variant calling Molecular genetics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3388 3388 187 187 1 1 1 1 1 1 1 1 3390 3390 189 189 False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell 2013-11-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes 2019-10-05 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 239 239 35 35 16 16 2 2 182 182 3 3 437 437 40 40 False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod 2014-02-18 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 Nucleic acid sequence analysis Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 548 548 18 18 0 0 0 0 548 548 18 18 False -clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw 2022-10-02 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 Multiple sequence alignment Phylogeny, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79867 80817 1675 1785 49493 87884 3703 7380 8797 9713 670 728 138157 178414 6048 9893 False -cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 513 813 18 35 2406 30579 156 1547 1353 1393 17 20 4272 32785 191 1602 False -clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ Statistics clustering_from_distmat 2024-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 1.1.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 5 5 0 0 0 0 0 0 0 0 12 12 5 5 False -cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap 2023-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl Comparison, Alignment Biology, Medicine 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2609 2609 3 3 0 0 0 0 0 0 0 0 2609 2609 3 3 False -cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv 2017-09-26 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 90 112 11 14 0 0 0 0 0 0 0 0 90 112 11 14 False -cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json 2024-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.1.0 cnv-vcf2json 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit 2023-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 Variant calling 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 618 618 177 177 0 0 0 0 0 0 0 0 618 618 177 177 False -codeml codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml 2017-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 Probabilistic sequence generation Phylogenetics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61197 61220 64 65 0 0 0 0 0 0 0 0 61197 61220 64 65 False -cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 316 355 25 29 0 0 0 0 0 0 0 0 316 355 25 29 False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac 2022-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.2 cojac 0.9.2 Genetic variation 2 0 3 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2758 2758 22 22 20 20 10 10 0 0 0 0 2778 2778 32 32 False -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold 2024-03-24 iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6771 6771 50 50 0 0 0 0 6771 6771 50 50 False -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome Up-to-date https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread 2017-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14 commet 24.7.14 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 273 40 40 0 0 0 0 0 0 0 0 273 273 40 40 False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 39518 40471 3555 3629 22007 24841 3536 4045 3969 4101 814 835 65494 69413 7905 8509 False -collection_column_join collection_column_join Column Join on Collections To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join Text Manipulation collection_column_join 2016-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 23979 25337 3827 4011 21671 25163 4645 5045 2939 3036 688 701 48589 53536 9160 9757 False -collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers Text Manipulation collection_element_identifiers 2018-06-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6905 7102 1620 1630 7761 7761 1897 1897 1157 1157 243 243 15823 16020 3760 3770 False -color_deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution 0.8 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 15 16 2 3 0 0 0 0 0 0 0 0 15 16 2 3 False -colorize_labels colorize_labels Colorize label map To update https://github.com/bmcv Imaging colorize_labels 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 3.2.1 networkx 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -column_arrange_by_header bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header 2015-03-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5356 5636 446 484 2026 2026 375 375 1400 1531 117 138 8782 9193 938 997 False -column_maker Add_a_column1 Compute an expression on every row To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker Text Manipulation column_maker 2019-06-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2940752 3907183 5422 6121 263254 737503 6095 13728 96478 97667 884 974 3300484 4742353 12401 20823 False -column_order_header_sort column_order_header_sort Sort Column Order by heading To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort Text Manipulation column_order_header_sort 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3735 3891 268 297 1923 1923 381 381 0 0 0 0 5658 5814 649 678 False -column_remove_by_header column_remove_by_header Remove columns by header To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header Text Manipulation column_remove_by_header 2017-04-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8331 8917 613 662 5206 5206 716 716 1976 1976 27 27 15513 16099 1356 1405 False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json 2018-03-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats 2017-11-08 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 2023-07-20 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python Aggregation Metagenomics, Molecular interactions, pathways and networks 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 530 530 65 65 8 8 6 6 0 0 0 0 538 538 71 71 False -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp 2015-06-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 221 5 28 0 0 0 0 0 0 0 0 39 221 5 28 False -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 Comparison Metagenomics, Gene and protein families 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 306 332 28 32 0 0 0 0 0 0 0 0 306 332 28 32 False -compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm 2023-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Transcriptomics, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 266 266 39 39 28 28 15 15 0 0 0 0 294 294 54 54 False -complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 187 233 15 20 495 4810 165 836 405 451 7 7 1087 5494 187 863 False -compose_text_param compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param 2019-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 45827 45831 689 691 7721 7721 303 303 1481 1481 121 121 55029 55033 1113 1115 False -compress_file compress_file Compress files. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file Text Manipulation compress_file 2022-02-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6343 6343 290 290 3674 3674 286 286 11832 11832 59 59 21849 21849 635 635 False -compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 85 96 9 10 0 0 0 0 316 334 8 8 401 430 17 18 False -compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 65 2 2 0 0 0 0 317 335 5 5 372 400 7 7 False -compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 0 3 0 0 0 0 0 0 0 0 0 35 0 3 False -concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 575128 575441 694 783 43420 85345 629 3508 19330 19418 104 117 637878 680204 1427 4408 False -concat_channels ip_concat_channels Concatenate images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels 0.3-1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 82 11 12 0 0 0 0 0 0 0 0 76 82 11 12 False -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets 2019-04-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 4822 4824 613 614 1317 1317 204 204 3088 3795 252 289 9227 9936 1069 1107 False -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired 2019-12-16 nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct 2022-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 Sequence clustering, Read binning Metagenomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2105 2105 155 155 0 0 0 0 0 0 0 0 2105 2105 155 155 False -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2173 28 368 195 205 8 8 242 2378 36 376 False -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign 2023-04-11 ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1184 1184 154 154 0 0 0 0 0 0 0 0 1184 1184 154 154 False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs 2015-11-26 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 23589 28986 1061 1200 23507 160693 2302 8699 5413 6446 251 329 52509 196125 3614 10228 False -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler 2018-12-07 lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.21 4 0 5 0 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 170 170 26 26 195 195 39 39 0 0 0 0 365 365 65 65 False -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi 0.0.4-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16077 16547 11 11 0 0 0 0 0 0 0 0 16077 16547 11 11 False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna 2017-11-01 rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -correlation cor2 Correlation for numeric columns To update Statistics correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 398 876 106 134 412 5568 105 755 192 239 21 27 1002 6683 232 916 False -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis 2020-12-08 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 280 307 110 124 712 1277 332 628 476 541 55 79 1468 2125 497 831 False -count_objects ip_count_objects Count Objects galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects 0.0.5-2 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 314 326 73 75 0 0 0 0 129 129 6 6 443 455 79 81 False -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants 2016-02-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1560 1725 43 58 4328 44209 193 2113 283 316 16 18 6171 46250 252 2189 False -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report 2017-10-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats 2015-07-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm 2022-04-26 iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 Local alignment Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1081 1081 151 151 0 0 0 0 0 0 0 0 1081 1081 151 151 False -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 False -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio 2019-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 Visualisation Sequence analysis, Genomics, Data visualisation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1052 1053 75 76 0 0 0 0 0 0 0 0 1052 1053 75 76 False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 False -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies Up-to-date http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap 2017-07-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.7.0 crossmap 0.7.0 5 0 6 0 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 2182 2182 331 331 5251 5251 903 903 0 0 0 0 7433 7433 1234 1234 False -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4066 4139 166 180 0 0 0 0 0 0 0 0 4066 4139 166 180 False -cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper 2020-10-14 nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9942 9942 26 26 0 0 0 0 0 0 0 0 9942 9942 26 26 False -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk 2019-08-27 nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 20 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cta cta_astro_tool Basic simulation of CTA telescope observations using gammapy package To update Astronomy cta_astro_tool 2024-04-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0.0.1+galaxy0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 196 211 41 48 1 447 1 161 0 0 0 0 197 658 42 209 False -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 False -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 False -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 False -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 False -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 False -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 False -cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund 2015-04-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1251 1803 98 166 3461 15159 486 2044 2425 3338 57 159 7137 20300 641 2369 False -cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular 2014-12-22 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 1208 43 97 1334 2683 101 479 0 0 0 0 2222 3891 144 576 False -curve_fitting ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1729 1744 144 146 450 450 72 72 361 361 12 12 2540 2555 228 230 False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1973168 2034965 11939 12833 352364 803522 12967 30199 128777 133584 2341 2572 2454309 2972071 27247 45604 False -cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt 2023-11-03 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.9 cutadapt 4.9 Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 259754 272370 11716 12601 334550 362356 18618 20162 64377 65986 3507 3627 658681 700712 33841 36390 False -cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Up-to-date https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv 2020-09-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 2.1.1 cutesv 2.1.1 Split read mapping, Genotyping, Structural variation detection Sequencing, Computer science 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 260 260 43 43 0 0 0 0 119 119 8 8 379 379 51 51 False -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 173 280 41 83 0 0 0 0 173 280 41 83 False -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 2019-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 10 0 10 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 10 0 92240 92240 2716 2716 179176 179176 5317 5317 12478 12478 394 394 283894 283894 8427 8427 False -das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 Read binning Metagenomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1323 1323 47 47 0 0 0 0 0 0 0 0 1323 1323 47 47 False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology 2021-07-27 ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles 0 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 967 967 308 308 0 0 0 0 0 0 0 0 967 967 308 308 False -data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga 2016-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation 2015-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 1 3 3 0 0 1 0 0 0 1 0 0 0 0 0 0 3 3 3 0 748586 760943 7066 7307 98089 112831 5306 6131 16235 16317 2161 2171 862910 890091 14533 15609 False -dbbuilder dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4813 5555 687 805 0 0 0 0 961 961 87 87 5774 6516 774 892 False -decontam decontam Removes decontamination features (ASVs/OTUs) using control samples decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. Classification Metagenomics, Microbial ecology, Sequencing To update https://github.com/benjjneb/decontam Metagenomics decontam 2024-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam 1.22 bioconductor-decontam 1.22.0 Classification Metagenomics, Microbial ecology, Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. Filtering Metagenomics To update https://github.com/cbib/decontaminator Machine Learning decontaminator 2023-01-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy Filtering Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 121 121 28 28 0 0 0 0 0 0 0 0 121 121 28 28 False -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -deepmicro deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro 2023-03-16 iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 558 558 7 7 0 0 0 0 0 0 0 0 558 558 7 7 False -deepsig deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig 2023-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 37 37 0 0 0 0 0 0 0 0 65 65 37 37 False -deepvariant deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant 2021-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2561 2561 325 325 2916 2916 460 460 0 0 0 0 5477 5477 785 785 False -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 False -delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33 40 6 7 0 0 0 0 0 0 0 0 33 40 6 7 False -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly 2020-10-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.3.1 Indel detection, Structural variation detection, Genotyping Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 1451 1451 288 288 0 0 0 0 0 0 0 0 1451 1451 288 288 False -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -detection_viz ip_detection_viz Detection Visualization galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 48 8 8 0 0 0 0 0 0 0 0 43 48 8 8 False -dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq 2022-10-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 18 18 0 0 0 0 0 0 0 0 89 89 18 18 False -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 False -dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator 2013-11-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 69 26 30 0 304 0 133 0 0 0 0 59 373 26 163 False -dia_umpire dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire 2015-08-26 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 33 4 4 0 0 0 0 134 134 4 4 162 167 8 8 False -dialignr dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr 2020-12-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 2 2 0 0 0 0 0 0 0 0 40 40 2 2 False -diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond 2021-03-21 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.10 Sequence alignment analysis Sequence analysis, Proteins 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 3 3 3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 61376 61746 1847 1895 23164 28729 1140 1556 63034 63034 522 522 147574 153509 3509 3973 False -diann diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann 2023-06-26 galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 72 72 14 14 0 0 0 0 171 171 14 14 243 243 28 28 False -diapysef diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef 2020-02-27 galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262 262 38 38 0 0 0 0 256 256 6 6 518 518 44 44 False -diff diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff 2020-03-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 362 362 99 99 23 23 17 17 0 0 0 0 385 385 116 116 False -diffacto diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto 2021-06-20 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 7 7 0 0 0 0 0 0 0 0 11 11 7 7 False -diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq Up-to-date http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2018-04-07 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 3.12.0 bioconductor-diffbind 3.12.0 Differential binding analysis ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7092 7663 606 652 14367 18624 1360 1916 1477 1640 69 84 22936 27927 2035 2652 False -diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -digestdb digestdb To update digestdb 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics 2023-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -directag_and_tagrecon To update directag_and_tagrecon 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco 2017-10-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 Protein sequence analysis Structure determination 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 358 406 124 139 1361 1361 384 384 0 0 0 0 1719 1767 508 523 False -divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 32 8 9 86 172 20 53 0 0 0 0 112 204 28 62 False -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot 2022-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver 2022-12-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina 2015-05-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 921 1626 4 31 0 0 0 0 0 0 0 0 921 1626 4 31 False -dose_responses dr_curve A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses To update https://github.com/bernt-matthias/mb-galaxy-tools Ecology dose_response_analysis_tool 2024-04-06 ufz https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 3.0.1 r-drc 3.0_1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct 2015-06-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot 2015-09-17 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 74 88 12 15 0 0 0 0 0 0 0 0 74 88 12 15 False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics Up-to-date https://github.com/WrightonLabCSU/DRAM Metagenomics dram 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.5.0 dram 1.5.0 Gene functional annotation Metagenomics, Biological databases, Molecular genetics 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 7358 7358 88 88 0 0 0 0 0 0 0 0 7358 7358 88 88 False -draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 216 47 52 0 0 0 0 183 213 22 31 372 429 69 83 False -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep 2020-01-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 Genome comparison Metagenomics, Sequence analysis 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 916 916 113 113 0 0 0 0 0 0 0 0 916 916 113 113 False -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1151 1151 184 184 356 356 77 77 3 3 1 1 1510 1510 262 262 False -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 141 8 11 136 141 8 11 False -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 124 124 7 7 124 124 7 7 False -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 123 5 7 121 123 5 7 False -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 132 7 8 131 132 7 8 False -dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 36 2 4 11 11 4 4 206 220 6 7 247 267 12 15 False -ear make_ear A tool to compile assembly reports and stastics from assembly pipeline To update https://github.com/ERGA-consortium/EARs/tree/main Sequence Analysis, Assembly erga_ear 2024-06-07 bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 24.10.15 reportlab 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 28 2 2 0 0 0 0 0 0 0 0 28 28 2 2 False -ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools 2016-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.1 six 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 406 133 163 1421 1421 547 547 0 0 0 0 1697 1827 680 710 False -ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper 2018-12-21 nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12996 12996 137 137 10 10 1 1 0 0 0 0 13006 13006 138 138 False -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 False -edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta 2022-10-16 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4495 4495 111 111 0 0 0 0 0 0 0 0 4495 4495 111 111 False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 2015-09-21 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 Sequence classification Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper 2019-11-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 3 1 0 34432 34437 1149 1152 42 42 2 2 21027 21027 413 413 55501 55506 1564 1567 False -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 False -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa 2022-11-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 2017-01-11 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis 107 107 107 107 107 107 107 107 0 0 0 0 0 0 0 0 0 0 107 0 0 107 0 0 0 107 0 0 0 0 0 0 107 107 107 0 143762 148864 4481 5039 151989 296028 13224 31140 24955 27001 2397 2705 320706 471893 20102 38884 False -ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload 2020-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.3 ena-upload-cli 0.7.4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 366 366 41 41 0 0 0 0 1302 1302 14 14 1668 1668 55 55 False -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch 2017-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 0 0 5 0 0 0 5 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1989 2302 367 453 0 0 0 0 0 0 0 0 1989 2302 367 453 False -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia 2020-09-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 2 4 7 0 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 738 738 98 98 1 1 1 1 42 42 4 4 781 781 103 103 False -ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep 2022-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 112.0 ensembl-vep 113.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3051 3051 171 171 0 0 0 0 0 0 0 0 3051 3051 171 171 False -eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie 2021-12-30 climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 4 4 0 0 0 0 0 0 0 0 45 45 4 4 False -epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg 2018-03-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 160 252 17 21 0 0 0 0 0 0 0 0 160 252 17 21 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability 2019-05-03 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 232 336 39 40 0 0 0 0 0 0 0 0 232 336 39 40 False -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete 2018-10-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 Phylogenetic tree editing Phylogenetics 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 820 966 89 106 0 0 0 0 0 0 0 0 820 966 89 106 False -evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. EvidenceModeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. Gene prediction Gene expression, Gene structure Up-to-date https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file Genome annotation evidencemodeler 2024-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler 2.1.0 evidencemodeler 2.1.0 Gene prediction Gene expression, Gene structure 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth 2019-11-08 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 517 517 61 61 2995 2995 184 184 0 0 0 0 3512 3512 245 245 False -exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate 2018-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1030 1072 185 188 1058 1058 189 189 922 922 35 35 3010 3052 409 412 False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 Conversion Taxonomy, Metabolomics, Biomarkers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5396 5938 580 607 628 628 168 168 519 519 107 107 6543 7085 855 882 False -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster 2016-01-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 278 337 34 45 0 1184 0 117 2402 2844 23 60 2680 4365 57 222 False -extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna 2016-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 9409 12735 813 923 20180 259099 2072 11791 168 611 20 63 29757 272445 2905 12777 False -ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms 2024-02-07 artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -falco falco A high throughput sequence QC analysis tool falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Up-to-date https://github.com/smithlabcode/falco/ Sequence Analysis falco 2024-04-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco 1.2.4 falco 1.2.4 Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4298 4298 34 34 0 0 0 0 0 0 0 0 4298 4298 34 34 False -fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene 2019-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 601 601 128 128 1165 1165 232 232 0 0 0 0 1766 1766 360 360 False -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit 2017-09-08 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 469 ucsc-fasplit 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3278 3361 460 478 6144 6144 595 595 1139 1139 183 183 10561 10644 1238 1256 False -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5191 5367 104 130 5191 5367 104 130 False -fasta_compute_length fasta_compute_length Compute sequence length To update https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length Fasta Manipulation fasta_compute_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.4 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8547 9136 978 1129 17748 51150 1404 5670 4239 4404 162 190 30534 64690 2544 6989 False -fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 39695 39742 242 255 13660 19007 600 1398 1521 1603 92 112 54876 60352 934 1765 False -fasta_extract fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract 2016-10-26 nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 10 10 1 1 0 0 0 0 1286 1827 144 181 1296 1837 145 182 False -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 47494 51924 889 997 50663 101663 1488 3742 3919 5601 241 276 102076 159188 2618 5015 False -fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 5235 5486 237 288 4060 25609 480 2039 816 1093 73 89 10111 32188 790 2416 False -fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30917 32191 1142 1257 36869 36869 1346 1346 5236 5236 230 230 73022 74296 2718 2833 False -fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 497 808 71 108 2249 5479 216 703 415 437 18 20 3161 6724 305 831 False -fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot 2016-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 164 179 42 47 758 905 128 170 0 0 0 0 922 1084 170 217 False -fasta_stats fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats 2018-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43726 44512 3104 3259 19941 19941 3693 3693 16788 18589 2467 2650 80455 83042 9264 9602 False -fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 108876 113638 1572 1793 82527 192112 2209 8565 5711 7649 275 334 197114 313399 4056 10692 False -fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani 2020-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 Genome alignment, Sequence similarity search Microbiology, Genetic variation 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6685 6685 603 603 0 0 0 0 0 0 0 0 6685 6685 603 603 False -fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib 2020-07-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk 2024-05-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 136 136 11 11 0 0 0 0 0 0 0 0 136 136 11 11 False -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp 2018-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 1624807 1625832 19811 19873 False -fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8604 8799 215 240 54200 75329 919 2957 1562 1680 76 85 64366 85808 1210 3282 False -fastq_filter fastq_filter Filter FASTQ reads by quality score and length To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15582 18350 690 771 40489 121585 2715 9239 4657 5793 214 287 60728 145728 3619 10297 False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id 2017-02-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_groomer fastq_groomer Convert between various FASTQ quality formats. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 92594 102535 2576 2995 179461 897457 9437 44701 15434 25533 664 1073 287489 1025525 12677 48769 False -fastq_info fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info 2021-09-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7560 7560 1266 1266 6539 6539 1581 1581 0 0 0 0 14099 14099 2847 2847 False -fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2488 3132 215 267 6241 14508 834 2121 4121 4592 131 158 12850 22232 1180 2546 False -fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 234 249 43 44 2648 8092 288 983 442 466 12 17 3324 8807 343 1044 False -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair 2022-03-17 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names 2014-05-05 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5873 8936 532 657 14738 20229 1889 2366 2316 2711 225 261 22927 31876 2646 3284 False -fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18216 19573 2348 2492 23484 25936 3482 3851 6207 6551 1402 1442 47907 52060 7232 7785 False -fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15628 17130 536 679 24157 58368 1954 5716 1941 2266 172 214 41726 77764 2662 6609 False -fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3169 3521 459 535 19309 30747 1410 3441 807 1023 219 247 23285 35291 2088 4223 False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1271 1393 131 176 12763 58819 2073 8850 430 479 32 51 14464 60691 2236 9077 False -fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 335 352 44 47 1583 9696 269 2229 1131 1254 15 27 3049 11302 328 2303 False -fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 17279 18386 3826 4062 55268 136888 6055 12590 7685 9356 1854 2043 80232 164630 11735 18695 False -fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer 2022-03-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastq_stats fastq_stats FASTQ Summary Statistics by column To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3858 4595 680 815 15213 81513 3159 14109 3855 4163 184 256 22926 90271 4023 15180 False -fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta 2016-09-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 36069 37805 1151 1234 45213 99852 2691 6370 8457 13335 408 609 89739 150992 4250 8213 False -fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 12895 14110 269 297 13315 30673 612 1810 5125 5373 64 87 31335 50156 945 2194 False -fastq_trimmer fastq_trimmer FASTQ Trimmer by quality To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10114 11383 582 665 23906 92351 1986 8818 1588 2607 108 212 35608 106341 2676 9695 False -fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window To update Fastq Manipulation fastq_trimmer_by_quality 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4881 6165 859 967 29458 99179 3455 11369 2171 2678 259 338 36510 108022 4573 12674 False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqc fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc 2017-12-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy1 fastqc 0.12.1 Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 0 1784056 1913280 41344 43940 2269843 3195869 90828 140008 410004 445555 14195 16026 4463903 5554704 146367 199974 False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fastqe fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe 2020-07-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 Sequencing quality control Sequence analysis, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5162 5162 2350 2350 10176 10176 4714 4714 2610 2610 991 991 17948 17948 8055 8055 False -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 3 0 0 0 0 0 8 0 3 False -fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 208349 217568 3421 3732 131388 245005 5108 13227 18655 18655 679 679 358392 481228 9208 17638 False -fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree 2018-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 65542 65631 1049 1071 25992 25992 2147 2147 6733 7339 649 745 98267 98962 3845 3963 False -fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1769 2020 88 101 6948 24960 358 2424 623 998 32 50 9340 27978 478 2575 False -fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16957 18124 225 260 37001 89126 919 2720 863 989 56 68 54821 108239 1200 3048 False -fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3140 3520 178 212 13975 117900 1198 6006 409 712 36 55 17524 122132 1412 6273 False -fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 64187 67981 326 349 87477 185555 781 3067 16563 17125 58 78 168227 270661 1165 3494 False -fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 174 272 61 92 4295 25068 1056 4180 1127 1171 70 89 5596 26511 1187 4361 False -fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics 2018-04-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2218 2344 168 206 20551 60032 3784 9866 2347 2460 234 256 25116 64836 4186 10328 False -fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2364 2526 180 214 6572 11745 303 1024 462 696 49 64 9398 14967 532 1302 False -fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10707 12597 356 415 21568 67304 574 1527 719 861 61 78 32994 80762 991 2020 False -fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer 2017-07-10 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 13584 14557 550 641 123676 206733 2034 8390 2819 4757 229 267 140079 226047 2813 9298 False -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates 2020-10-21 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 264 264 69 69 34 34 11 11 103 103 1 1 401 401 81 81 False -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf 2023-01-11 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 385 385 46 46 587 587 107 107 58 58 5 5 1030 1030 158 158 False -feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment 2021-11-22 galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 1 1 0 0 0 0 0 0 0 0 18 18 1 1 False -featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.13.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22308 22388 16 19 350 13711 54 349 0 0 0 0 22658 36099 70 368 False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 False -feelnc feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc 2018-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 Annotation, Classification Functional, regulatory and non-coding RNA 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 1500 95 99 797 797 116 116 59 59 3 3 2231 2356 214 218 False -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko 2018-04-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht 2017-10-11 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit 2017-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi 2017-11-21 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 1 1 False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 False -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6690 8818 554 612 0 0 0 0 0 0 0 0 6690 8818 554 612 False -filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 26717 29932 1026 1072 42990 42990 1176 1176 9619 9619 230 230 79326 82541 2432 2478 False -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds 2021-01-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density 2015-11-23 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats 2017-10-12 nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23 24 9 10 62 635 26 241 2 2 2 2 87 661 37 253 False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf 2015-08-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -filtlong filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong 2018-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 Filtering, Sequencing quality control 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53310 53944 1499 1575 25043 25043 726 726 10824 10824 593 593 89177 89811 2818 2894 False -find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 10 12 3 1787 1 204 0 0 0 0 65 1857 11 216 False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats 2015-08-14 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -find_subsequences bg_find_subsequences To update find_subsequences 2015-03-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 784 69 79 2820 3047 323 361 20 20 1 1 3394 3851 393 441 False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair 2020-11-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1985 1985 41 41 0 0 0 0 0 0 0 0 1985 1985 41 41 False -flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 589 731 51 63 2445 32847 304 2549 1214 1294 15 22 4248 34872 370 2634 False -flash flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash 2017-09-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22017 22304 239 255 9399 14886 462 709 4 4 1 1 31420 37194 702 965 False -flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq 2017-12-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 Label-free quantification Proteomics experiment, Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 661 715 52 54 0 0 0 0 167 167 15 15 828 882 67 69 False -flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. Up-to-date https://github.com/BIMSBbioinfo/flexynesis/tree/main Machine Learning, Statistics, Systems Biology flexynesis 2024-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0.2.10 flexynesis 0.2.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 2 2 0 0 0 0 0 0 0 0 9 9 2 2 False -flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. To update https://github.com/bgruening/galaxytools/tree/master/tools/cflux Machine Learning black_forest_labs_flux 2024-10-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -flye flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye 2018-09-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.5 flye 2.9.5 Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32514 32675 3379 3422 19434 19434 2537 2537 9843 9843 1624 1624 61791 61952 7540 7583 False -footprint footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint 2017-04-18 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 5 5 0 0 0 0 0 0 0 0 57 57 5 5 False -format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 189 203 57 60 0 0 0 0 0 0 0 0 189 203 57 60 False -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output 2022-10-19 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 Formatting Taxonomy, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5940 6474 558 608 0 0 0 0 0 0 0 0 5940 6474 558 608 False -fraggenescan fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan 2017-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 Gene prediction Genetics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1257 1450 150 162 0 0 0 0 1052 1052 45 45 2309 2502 195 207 False -fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. Up-to-date https://fragpipe.nesvilab.org/ Proteomics fragpipe 2023-05-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 20.0 fragpipe 20.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 9 9 0 0 0 0 0 0 0 0 64 64 9 9 False -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy 2019-11-11 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Up-to-date https://github.com/ekg/freebayes Variant Analysis freebayes 2017-01-23 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.8 freebayes 1.3.8 Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 149715 171093 8158 8794 144708 256315 15996 25107 19156 21936 2251 2571 313579 449344 26405 36472 False -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec 2020-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk Copy number estimation, Variant calling, Genome alignment Oncology, Human genetics, Data mining 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 748 748 91 91 0 0 0 0 12 12 1 1 760 760 92 92 False -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset RNA-Seq quantification Metagenomics Up-to-date https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja 2022-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.5.1 freyja 1.5.1 RNA-Seq quantification Metagenomics 2 0 4 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 21757 21757 101 101 217 217 21 21 0 0 0 0 21974 21974 122 122 False -frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing To update http://frogs.toulouse.inrae.fr/ Metagenomics frogs 2023-04-26 frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 5.0.0 Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing 0 0 0 28 0 0 0 28 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox 2018-06-05 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 2019-07-31 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution 2019-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 578 578 34 34 0 0 0 0 578 578 34 34 False -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation 2021-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 Genome annotation Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 8648 8648 1408 1408 32 32 6 6 6406 6406 597 597 15086 15086 2011 2011 False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 False -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 2021-12-29 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 2019-10-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3463 3463 452 452 9040 9040 1639 1639 0 0 0 0 12503 12503 2091 2091 False -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks 2018-04-11 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 466 466 62 62 466 466 62 62 False -gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization 2024-03-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor 2021-09-16 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor 2023-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal 2019-02-25 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 0 0 8 8 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 1409 1498 39 42 0 0 0 0 0 0 0 0 1409 1498 39 42 False -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp 2017-06-23 iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko 2020-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 723 723 235 235 0 0 0 0 786 786 95 95 1509 1509 330 330 False -gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini 2019-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 Sequence analysis, Genetic variation analysis Sequence analysis 1 2 2 2 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 4967 5475 1863 1992 992 1118 279 370 3756 3811 423 425 9715 10404 2565 2787 False -genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta 2020-08-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 4 4 2 2 221 2905 23 279 0 0 0 0 225 2909 25 281 False -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 Variant Analysis genehunter_modscore 2017-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio 2023-06-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 101 101 25 25 0 0 0 0 59 59 6 6 160 160 31 31 False -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services 2023-04-07 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.16 genoboo 0.4.16 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 115 124 29 30 518 1029 102 261 184 198 14 17 817 1351 145 308 False -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 660 104 197 0 0 0 0 445 660 104 197 False -genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform 2019-09-12 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 68 68 4 4 0 0 0 0 0 0 0 0 68 68 4 4 False -genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. Sequence annotation, Taxonomic classification Sequence analysis To update https://github.com/apcamargo/genomad/ Metagenomics genomad 2024-06-17 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad 1.8.0 genomad 1.8.1 Sequence annotation, Taxonomic classification Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -genomescope genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0.1 genomescope2 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3181 3181 665 665 2112 2112 435 435 1622 1622 148 148 6915 6915 1248 1248 False -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 False -genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich 2019-07-05 iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3534 3577 402 405 2840 2840 419 419 571 571 31 31 6945 6988 852 855 False -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage 2018-06-13 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3768 325011 1462 2044 9350 242043 2201 6583 787 1070 119 146 13905 568124 3782 8773 False -get_hrun get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 746 746 136 136 0 0 0 0 1504 1504 244 244 2250 2250 380 380 False -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs 2018-09-10 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 290 20 86 0 0 0 0 70 290 20 86 False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 237 24 61 0 0 0 0 74 237 24 61 False -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst 2015-12-03 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1542 1542 159 159 0 0 0 0 587 587 64 64 2129 2129 223 223 False -gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9664 9775 763 765 5623 5623 493 493 1000 1000 135 135 16287 16398 1391 1393 False -gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats 2022-03-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.8 gfastats 1.3.8 Data handling Computational biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11748 11748 767 767 6560 6560 397 397 2556 2556 106 106 20864 20864 1270 1270 False -gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase 2015-05-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 806 812 68 68 197 197 37 37 132 132 12 12 1135 1141 117 117 False -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 False -gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed 2018-01-10 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1375 2230 329 347 1071 1071 362 362 492 492 64 64 2938 3793 755 773 False -gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread 2019-10-29 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12828 13716 1740 1829 15217 23818 2588 3486 4423 4423 732 732 32468 41957 5060 6047 False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base Visualisation Data visualisation 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 24606 25662 3463 3630 26805 26808 5143 5144 8174 8237 1259 1279 59585 60707 9865 10053 False -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset 2022-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 Database search, ID mapping Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 490 682 74 109 127 14058 20 1798 0 0 0 0 617 14740 94 1907 False -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis 2017-11-28 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 Sequence analysis, Genetic variation analysis Sequence analysis 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 4343 4343 407 407 0 0 0 0 0 0 0 0 4343 4343 407 407 False -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 11 11 6 6 85 984 29 230 10 11 7 8 106 1006 42 244 False -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali 2020-03-30 nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -goenrichment goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation 2018-12-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 Gene-set enrichment analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5800 6212 826 871 7756 7756 1048 1048 1149 1149 215 215 14705 15117 2089 2134 False -goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq 2018-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 Gene functional annotation RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20207 21960 2807 3139 24488 26198 3066 3321 4155 4155 545 545 48850 52313 6418 7005 False -gotohscan rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan 2015-07-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 72 5 7 0 0 0 0 0 0 0 0 34 72 5 7 False -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 4001 4001 614 614 7882 7882 1238 1238 0 0 0 0 11883 11883 1852 1852 False -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 False -graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed 2019-12-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 78 78 6 6 120 120 43 43 0 0 0 0 198 198 49 49 False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick 2016-12-26 bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.45 graphicsmagick 1.3.26 1 0 3 0 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1725 2708 97 99 2 2 2 2 0 0 0 0 1727 2710 99 101 False -graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan 2017-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 9816 10927 1285 1350 1273 1273 368 368 1104 1104 242 242 12193 13304 1895 1960 False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap 2018-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.4 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 7012 7344 323 338 0 0 0 0 0 0 0 0 7012 7344 323 338 False -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot 2018-05-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy2 graphprot 1.1.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 463 484 18 19 0 0 0 0 0 0 0 0 463 484 18 19 False -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs 2022-03-22 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 14 8 15 0 14 8 15 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 184067 184203 3441 3451 9382 9382 1438 1438 10325 10325 648 648 203774 203910 5527 5537 False -groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Up-to-date https://github.com/will-rowe/groot Metagenomics groot 2024-05-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot 1.1.2 groot 1.1.2 Antimicrobial resistance prediction Metagenomics, Microbiology 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 False -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation 2018-04-24 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 377 400 17 17 0 0 0 0 0 0 0 0 377 400 17 17 False -gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. Data handling, Mapping, Generation Computational biology Up-to-date https://github.com/nick-youngblut/gtdb_to_taxdump Metagenomics gtdb_to_taxdump 2024-08-25 iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Data handling, Mapping, Generation Computational biology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk 2022-12-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.4.0 gtdbtk 2.4.0 Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 476 476 87 87 0 0 0 0 588 588 74 74 1064 1064 161 161 False -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1982 1983 323 324 1040 1040 343 343 205 205 38 38 3227 3228 704 705 False -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 2018-05-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 469 Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 8329 9363 3336 3828 8009 8009 3130 3130 1577 1577 344 344 17915 18949 6810 7302 False -gubbins gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3690 3811 326 336 3323 3323 235 235 1895 2429 234 258 8908 9563 795 829 False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller 2020-11-18 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 6.5.7+galaxy0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 7 7 1 1 False -gvcftools gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. To update https://github.com/sequencing/gvcftools Variant Analysis 2016-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis 2019-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 Deposition, Analysis, Annotation GWAS study 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization 2021-02-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 7303 7303 222 222 20 20 2 2 0 0 0 0 7323 7323 224 224 False -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 349 359 32 33 364 364 53 53 0 0 0 0 713 723 85 86 False -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 2022-10-19 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 Haplotype mapping, Variant classification 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 103 4 4 103 103 4 4 False -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog 2022-09-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 Genome assembly, Optimisation and refinement Sequence assembly, Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 502 502 66 66 0 0 0 0 0 0 0 0 502 502 66 66 False -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy 2022-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hardklor hardklor, kronik Hardklör To update Proteomics hardklor 2016-04-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 98 111 5 8 0 0 0 0 0 0 0 0 98 111 5 8 False -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 2018-07-22 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg 2015-08-05 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 243 263 54 57 0 0 0 0 0 0 0 0 243 263 54 57 False -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser 2015-08-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 266 293 22 25 0 0 0 0 0 0 0 0 266 293 22 25 False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 2019-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.2.0 r-gplots 2.17.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46700 50808 4645 5114 64214 70429 5799 6830 7783 7912 704 724 118697 129149 11148 12668 False -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 False -helixer helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer 2023-06-14 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 Gene prediction, Genome annotation Sequence analysis, Gene transcripts 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 267 267 39 39 0 0 0 0 80 80 7 7 347 347 46 46 False -hess hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope To update Astronomy hess_astro_tool 2024-02-19 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0.0.2+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 145 1794 33 397 0 0 0 0 145 1794 33 397 False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 119 265 16 60 0 0 0 0 119 265 16 60 False -hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard To update https://github.com/VariantEffect/hgvsParseR/tree/master Variant Analysis hgvsparser 2024-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6346 6346 2 2 0 0 0 0 0 0 0 0 6346 6346 2 2 False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer 2020-03-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.5 hicexplorer 3.7.5 38 38 38 4 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 44449 68602 3236 4177 46 46 21 21 1328 1328 67 67 45823 69976 3324 4265 False -hicstuff hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices Up-to-date https://github.com/koszullab/hicstuff Sequence Analysis 2022-11-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.2.3 hicstuff 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk 2024-02-03 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 1.0.0 hictk 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 9 9 0 0 0 0 0 0 0 0 17 17 9 9 False -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup 2017-03-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 7 0 7 0 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 901 1020 160 184 440 440 111 111 0 0 0 0 1341 1460 271 295 False -hifiasm hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm 2024-07-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 0.19.9 hifiasm 0.20.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1819 1819 539 539 1334 1334 389 389 2472 2472 137 137 5625 5625 1065 1065 False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta 2023-01-18 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 Sequence assembly Sequence assembly, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 156 156 20 20 0 0 0 0 220 220 11 11 376 376 31 31 False -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap 2019-07-20 artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hirondelle_crim_ogc_api_processes hirondelle_crim This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. To update https://github.com/AquaINFRA/galaxy Ecology 2024-06-07 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes 0.2.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat 2015-05-13 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 0 12 0 0 0 0 0 0 0 0 0 228 0 12 False -hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 2020-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 Sequence alignment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 337151 353499 10046 10719 699868 896164 26656 34018 87016 94859 5302 5695 1124035 1344522 42004 50432 False -histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3748 4661 866 1002 5993 48272 1507 7101 549 746 152 253 10290 53679 2525 8356 False -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.8.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace 2015-12-10 nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis 2016-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 35919 36952 1283 1321 0 0 0 0 3023 3023 180 180 38942 39975 1463 1501 False -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse 2021-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 Sequence motif discovery 0 0 5 4 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 8531 8531 633 633 0 0 0 0 0 0 0 0 8531 8531 633 633 False -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip 2022-10-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 98 98 19 19 0 0 0 0 0 0 0 0 98 98 19 19 False -htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count 2017-01-06 lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 Nucleic acid sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 144907 168824 3703 4366 213407 346792 10798 16485 27209 33124 2613 2854 385523 548740 17114 23705 False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann 2021-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.9 humann 3.9 Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics 6 10 10 10 6 10 10 10 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 26659 26659 2067 2067 865 865 174 174 3238 3238 351 351 30762 30762 2592 2592 False -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper 2023-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.3.0 Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1571 1571 3 3 0 0 0 0 144 144 4 4 1715 1715 7 7 False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie 2023-02-27 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics 2021-04-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks 17 2 17 2 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 11429 11429 428 428 7751 7751 676 676 715 715 58 58 19895 19895 1162 1162 False -hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo 2021-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 Optimisation and refinement, Genome assembly Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 473 473 93 93 0 0 0 0 0 0 0 0 473 473 93 93 False -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen 2022-01-04 iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -idba_ud idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 Sequence assembly Sequence assembly 3 0 3 3 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1200 1220 187 195 1588 1588 267 267 0 0 0 0 2788 2808 454 462 False -idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert 2019-02-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 241 276 24 33 0 0 0 0 0 0 0 0 241 276 24 33 False -idr idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr 2017-08-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2953 3027 109 114 1710 1710 199 199 0 0 0 0 4663 4737 308 313 False -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids 2020-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.45 omero-py 5.11.1 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 404 404 37 37 0 0 0 0 24 24 1 1 428 428 38 38 False -iedb_api iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api 2020-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1539 1539 35 35 0 0 0 0 0 0 0 0 1539 1539 35 35 False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -image_info ip_imageinfo Extracts image metadata python-bioformats To update https://github.com/bmcv Imaging image_info 2019-07-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info 5.7.1 bftools 6.7.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 273 659 101 102 0 0 0 0 153 153 15 15 426 812 116 117 False -image_math image_math Process images using arithmetic expressions To update https://github.com/bmcv Imaging image_math 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math 1.26.4 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 2 2 0 0 0 0 0 0 0 0 58 58 2 2 False -image_registration_affine ip_image_registration Intensity-based Image Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine 2020-12-29 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine 0.0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 5 5 0 0 0 0 0 0 0 0 16 16 5 5 False -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis 2019-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis 0.1-2 pandas Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 21409 21849 10 12 0 0 0 0 0 0 0 0 21409 21849 10 12 False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 2020-09-09 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 20240614 Image analysis, Image annotation, Visualisation Imaging 0 0 27 0 0 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 1731 1731 109 109 0 0 0 0 0 0 0 0 1731 1731 109 109 False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero 2023-02-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 18 22 1 1 44 292 3 21 0 0 0 0 62 314 4 22 False -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 False -infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal 2015-05-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 59700 112582 223 282 0 0 0 0 1157 1221 34 35 60857 113803 257 317 False -influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows To update https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager 2024-02-09 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.3 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si 2020-04-17 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.1.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -instagraal instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal 2022-11-10 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 157 157 14 14 0 0 0 0 0 0 0 0 157 157 14 14 False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain 2021-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 SNP detection, Genome comparison Mapping, Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 102 102 16 16 0 0 0 0 0 0 0 0 102 102 16 16 False -intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna 2019-01-10 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.1 intarna 3.4.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3071 7652 41 47 0 0 0 0 0 0 0 0 3071 7652 41 47 False -integron_finder integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.5 integron_finder 2.0.5 Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 55149 55149 161 161 0 0 0 0 6085 6085 73 73 61234 61234 234 234 False -intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter To update https://github.com/intermine Convert Formats intermine_galaxy_exchange 2018-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 46 6 12 72 87 13 15 108 108 1 1 217 241 20 28 False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology 2024-01-05 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 7 7 0 0 0 0 0 0 0 0 70 70 7 7 False -interproscan interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan 2021-11-15 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34689 55189 1634 1713 65 65 15 15 10897 10897 607 607 45651 66151 2256 2335 False -intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 20472 349984 2351 3007 45587 778988 4359 14116 6087 7417 484 561 72146 1136389 7194 17684 False -interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf 2020-07-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.13.0 Sequence analysis 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 107 7 10 758 19538 87 1246 16 24 2 2 806 19669 96 1258 False -intervene intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene 2018-09-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 Sequence comparison, Sequence visualisation Computational biology 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1557 1607 278 292 4458 4458 458 458 0 0 0 0 6015 6065 736 750 False -iphop iphop_predict Integrated Phage Host Prediction iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. Sample comparison Up-to-date https://bitbucket.org/srouxjgi/iphop/ Metagenomics iphop 2024-10-14 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop 1.3.3 iphop 1.3.3 Sample comparison 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo 2019-10-03 lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -iqtree iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree 2017-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.6 iqtree 2.3.6 Phylogenetic analysis, Sequence analysis Phylogenetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28279 28481 1623 1646 24662 24662 2093 2093 9780 10086 979 992 62721 63229 4695 4731 False -irissv irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.21 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 29 8 8 0 0 0 0 0 0 0 0 29 29 8 8 False -isescan isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan 2022-09-01 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 Structural variation detection Genomics, Sequence analysis, Genetic variation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59386 59386 151 151 56 56 1 1 4741 4741 59 59 64183 64183 211 211 False -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 False -isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib 2023-10-26 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -isoplot isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot 2021-07-12 workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 3 3 0 0 0 0 0 0 0 0 4 4 3 3 False -itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx 2022-05-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1426 1426 71 71 0 0 0 0 0 0 0 0 1426 1426 71 71 False -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar 2020-06-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.3 ivar 1.4.3 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 1252220 1252220 2366 2366 126027 126027 2496 2496 41901 41901 993 993 1420148 1420148 5855 5855 False -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics 2017-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 675 690 27 28 159 251 29 49 383 383 12 12 1217 1324 68 89 False -jasminesv jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 32 9 9 53 53 19 19 0 0 0 0 85 85 28 28 False -jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 Genome visualisation Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 21153 22174 5514 5779 17428 17428 6458 6458 15673 17267 3248 3786 54254 56869 15220 16023 False -jbrowse jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container 2016-11-08 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool jbrowse_2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Up-to-date https://jbrowse.org Sequence Analysis jbrowse2 2024-06-04 fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 2.15.4 jbrowse2 2.15.4 Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1312 1312 219 219 116 116 58 58 37 37 6 6 1465 1465 283 283 False -jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats 2018-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.16 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2747 2926 596 637 2311 2311 741 741 1145 1145 469 469 6203 6382 1806 1847 False -jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish 2021-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 k-mer counting Sequence analysis, Genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1825 1825 237 237 0 0 0 0 971 971 56 56 2796 2796 293 293 False -join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15624 330820 1864 2438 52317 513688 10198 39421 1329 1645 213 289 69270 846153 12275 42148 False -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id Text Manipulation join_files_by_id 2017-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy 2017-11-26 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1980 2697 345 410 0 0 0 0 1081 1081 44 44 3061 3778 389 454 False -jq jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq 2017-06-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 660 2374 61 63 336 336 82 82 281 281 11 11 1277 2991 154 156 False -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job 2021-12-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff 2017-09-27 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip 2018-05-16 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit 2021-02-11 iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7179 7179 509 509 11138 11138 1145 1145 0 0 0 0 18317 18317 1654 1654 False -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 False -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive 2017-04-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter 2017-03-13 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect 2017-02-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 Multiple sequence alignment Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 379 53 53 8259 8259 271 271 0 0 0 0 8638 8638 324 324 False -kegalign kegalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/galaxyproject/KegAlign Next Gen Mappers kegalign 2024-08-29 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign 0.1.2.7 kegalign-full 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 5 5 1 1 False -kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 70 4 4 207 334 27 71 0 0 0 0 269 404 31 75 False -kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 157 26 30 268 707 83 248 0 0 0 0 412 864 109 278 False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer 2015-11-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 Standardisation and normalisation, De-novo assembly Sequence assembly 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 1995 2091 174 193 1430 1430 389 389 1580 1580 56 56 5005 5101 619 638 False -king king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king 2021-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 False -kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing To update https://github.com/katholt/Kleborate/wiki Metagenomics kleborate 2022-09-09 iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 3.1.0 Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 503 503 58 58 0 0 0 0 0 0 0 0 503 503 58 58 False -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma 2019-10-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.4.14 kma 1.4.15 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot 2023-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan 2020-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 Sequence analysis, Gene functional annotation Genomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1342 1342 63 63 0 0 0 0 0 0 0 0 1342 1342 63 63 False -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 Taxonomic classification Taxonomy, Metagenomics 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 48136 48164 2754 2760 59952 130398 5869 8654 29008 31148 1936 2200 137096 209710 10559 13614 False -kraken2 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics Up-to-date http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 2019-03-06 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.3 kraken2 2.1.3 Taxonomic classification Taxonomy, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 271367 271786 6384 6409 101752 101752 4662 4662 53562 53562 1663 1663 426681 427100 12709 12734 False -kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax 2015-08-05 devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23008 23014 1060 1061 16194 24490 1719 2168 14898 14898 436 436 54100 62402 3215 3665 False -kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom 2022-09-03 iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3185 3185 495 495 0 0 0 0 385 385 48 48 3570 3570 543 543 False -kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report 2016-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 Visualisation, Classification Metagenomics, Taxonomy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3981 3986 769 771 4087 5610 991 1284 88 88 41 41 8156 9684 1801 2096 False -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools 2023-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 Visualisation, Aggregation Taxonomy, Metagenomics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 48516 48516 2373 2373 8787 8787 943 943 4369 4369 393 393 61672 61672 3709 3709 False -krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 Multilocus sequence typing, k-mer counting Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -label_to_binary label_to_binary Convert label map to binary image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging label_to_binary 2024-03-13 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -labelimage2points ip_labelimage_to_points Label Image to Points galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 34 38 2 2 0 0 0 0 0 0 0 0 34 38 2 2 False -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -landmark_registration ip_landmark_registration Landmark Registration galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration 2019-02-04 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration 0.1.0-2 scikit-image Image analysis Imaging, Bioinformatics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 887 927 13 15 4 4 3 3 0 0 0 0 891 931 16 18 False -last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1584 Sequence alignment Comparative genomics 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 329 329 94 94 0 0 0 0 0 0 0 0 329 329 94 94 False -lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz 2018-02-19 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 Sequence alignment, Read mapping Genomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 77409 84356 447 475 156658 193590 870 3511 38579 38780 173 203 272646 316726 1490 4189 False -lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads 2012-11-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 9 3 4 0 0 0 0 8 10 5 5 15 19 8 9 False -lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 89 137 4 20 118 6136 15 1112 0 0 0 0 207 6273 19 1132 False -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie 2022-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 147 159 46 48 793 1538 101 314 0 4 0 3 940 1701 147 365 False -legsta legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta 2022-02-21 iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 Sequence analysis Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 8 8 0 0 0 0 0 0 0 0 92 92 8 8 False -length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content 2016-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4349 4466 666 698 2093 2286 928 998 201 201 77 77 6643 6953 1671 1773 False -lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant 2018-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 78 116 12 19 0 0 0 0 0 0 0 0 78 116 12 19 False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter 2016-06-04 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Whole genome sequencing, DNA, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 149 171 27 30 0 0 0 0 0 0 0 0 149 171 27 30 False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 False -lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot 2023-07-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 4 4 0 0 0 0 0 0 0 0 39 39 4 4 False -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 146 1103 31 271 0 0 0 0 146 1103 31 271 False -links links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links 2022-02-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 512 512 126 126 0 0 0 0 480 480 65 65 992 992 191 191 False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs Up-to-date http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 2.0.1 locarna 2.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 314 350 36 46 0 0 0 0 0 0 0 0 314 350 36 46 False -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis 2019-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 5 5 5 4 5 5 5 4 0 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4176367 4176367 4301 4301 509615 509615 8213 8213 106342 106342 1815 1815 4792324 4792324 14329 14329 False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 173 12 48 0 0 0 0 64 173 12 48 False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis 2018-06-06 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -longorf longORF obtain longest ORF in six-frame translations To update Sequence Analysis longorf 2018-06-01 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype 2018-05-07 iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 Sequence analysis, Genotyping Genotype and phenotype 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 822 822 14 14 0 0 0 0 0 0 0 0 822 822 14 14 False -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 2021-06-08 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.34.1 Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1219 1219 182 182 0 0 0 0 37 37 4 4 1256 1256 186 186 False -ltq_iquant_cli To update ltq_iquant_cli 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove 2020-07-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv 2020-11-12 iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 1534 1534 199 199 0 0 0 0 0 0 0 0 1534 1534 199 199 False -lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 1.3 lumpy-sv 0.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet 2023-10-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 44 11 11 0 0 0 0 0 0 0 0 44 44 11 11 False -maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 2021-11-05 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 1.18.0 bioconductor-maaslin2 1.18.0 Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2835 2835 59 59 0 0 0 0 0 0 0 0 2835 2835 59 59 False -macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 2018-01-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 87810 96069 4980 5629 153500 227569 12946 18825 10988 12301 692 807 252298 335939 18618 25261 False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 356 6 28 0 0 0 0 85 356 6 28 False -maf_stats maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats 2020-08-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 15 21 7 9 227 2470 52 464 1 1 1 1 243 2492 60 474 False -mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft 2023-11-06 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.526 mafft 7.525 Multiple sequence alignment Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 0 2 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 172433 174456 1865 1951 108640 122790 4266 5521 20027 20027 1172 1172 301100 317273 7303 8644 False -maftoaxt maftoaxt Convert dataset from MAF to axt format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_maftoaxt 2024-07-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt 469 ucsc-maftoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing 2018-03-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 Genetic variation analysis Genetics, Genetic variation, Genomics 3 5 5 5 3 5 5 5 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 11761 12093 873 889 5762 5762 473 473 5610 5610 343 343 23133 23465 1689 1705 False -mahotas_features ip_mahotas_features Compute image features using mahotas. mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging mahotas_features 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features 0.7-2 mahotas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 6 0 0 0 0 0 0 0 0 39 44 6 6 False -make_data_paper_sketches data_paper_from_EML This tool derived from the R Shiny App MetaShRIMPS is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. To update https://github.com/TanguyGen/emldown Ecology Make data paper sketches from EML 2024-10-15 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches 0.1.0+galaxy0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr 2018-11-06 peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -maker maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis 2017-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 Genome annotation Genomics, DNA, Sequence analysis 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6417 6861 1315 1366 7235 7235 1858 1858 4112 4112 902 902 17764 18208 4075 4126 False -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant 2018-08-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1452 3822 61 68 0 0 0 0 1065 1065 39 39 2517 4887 100 107 False -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run 2021-11-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 9 9 0 0 0 0 0 0 0 0 24 24 9 9 False -manta manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta 2023-06-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 218 218 34 34 0 0 0 0 0 0 0 0 218 218 34 34 False -map_param_value map_param_value Map a parameter value to another value To update Text Manipulation map_param_value 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3780 3780 67 67 1012 1012 57 57 105 105 3 3 4897 4897 127 127 False -map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 44 6 7 0 0 0 0 0 0 0 0 38 44 6 7 False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats 2022-06-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq 2023-08-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1b perl k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7871 7871 32 32 0 0 0 0 0 0 0 0 7871 7871 32 32 False -marine_omics sanntis_marine The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data Up-to-date https://github.com/Finn-Lab/SanntiS Ecology 2024-07-26 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics 0.9.3.5 sanntis 0.9.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 4 4 0 0 0 0 0 0 0 0 51 51 4 4 False -mash mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics 2019-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 Sequence distance matrix generation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 10119 10119 61 61 19 19 9 9 647 647 7 7 10785 10785 77 77 False -mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap 2024-02-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 894 894 12 12 81 81 5 5 0 0 0 0 975 975 17 17 False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 False -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms 2023-12-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.27.0 matchms 0.27.0 Spectral library search, Format validation, Filtering Metabolomics 2 14 14 11 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1620 1620 70 70 27 27 8 8 1685 1685 12 12 3332 3332 90 90 False -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover 2019-11-19 nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer 2023-12-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 2 2 0 0 0 0 0 0 0 0 8 8 2 2 False -maxbin2 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 2019-10-24 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 Sequence assembly Metagenomics, Sequence assembly, Microbiology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 2798 2798 314 314 2452 2452 508 508 914 914 89 89 6164 6164 911 911 False -maxquant maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant 2021-08-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6863 7021 1251 1264 2798 2798 543 543 3189 3189 352 352 12850 13008 2146 2159 False -mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 13 13 0 0 0 0 0 0 0 0 35 35 13 13 False -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis 2018-10-08 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis 10 5 10 0 10 5 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 3209 3268 318 326 182 182 51 51 397 397 39 39 3788 3847 408 416 False -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter 2018-10-13 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26720 26762 251 253 784 784 54 54 977 977 53 53 28481 28523 358 360 False -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter 2019-10-07 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 174 19 19 6 6 4 4 441 441 7 7 621 621 30 30 False -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj 2020-06-24 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 8 8 63 63 4 4 0 0 0 0 99 99 12 12 False -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea 2015-07-29 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 73 86 5 5 0 0 0 0 0 0 0 0 73 86 5 5 False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 3 3 0 0 0 0 0 0 0 0 20 25 3 3 False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis 2020-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 2.0.1 Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 117975 117975 1693 1693 55063 55063 796 796 9325 9325 639 639 182363 182363 3128 3128 False -medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source 2023-12-12 ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 0 0 0 0 0 0 0 0 27 27 9 9 False -megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 743 816 103 141 292 2868 82 459 0 0 0 0 1035 3684 185 600 False -megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 12692 13292 1349 1400 16645 16645 2140 2140 6214 6214 431 431 35551 36151 3920 3971 False -megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg 2018-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 Genome assembly Metagenomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 513 557 152 155 74 74 35 35 10 10 4 4 597 641 191 194 False -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan 2021-11-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 Sequence analysis, Taxonomic classification Sequence analysis 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 4130 4130 447 447 0 0 0 0 0 0 0 0 4130 4130 447 447 False -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme 2018-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.5.6 meme 5.5.7 Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability 3 0 4 0 3 0 4 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 20990 22979 762 892 10975 25929 1551 3249 0 0 0 0 31965 48908 2313 4141 False -meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip 2018-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6413 7000 705 743 7260 7260 1171 1171 0 0 0 0 13673 14260 1876 1914 False -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco 2018-06-11 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype 2023-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 Multilocus sequence typing Microbiology, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 565922 566630 418 441 45844 107523 671 4353 19828 19994 100 137 631594 694147 1189 4931 False -merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 20905 31051 1906 2128 21780 132833 885 3172 1524 1925 122 152 44209 165809 2913 5452 False -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage 2019-01-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage 0.3-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 25 2 3 0 0 0 0 0 0 0 0 18 25 2 3 False -merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin 2020-04-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 Haplotype mapping GWAS study, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury 2021-04-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3150 3150 477 477 730 730 196 196 1183 1183 151 151 5063 5063 824 824 False -meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 k-mer counting Whole genome sequencing, Genomics, Sequence analysis 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 20 20 0 0 0 0 0 0 0 0 126 126 20 20 False -metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing To update https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.17 Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing 2 1 2 2 2 1 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 6135 6135 382 382 881 881 151 151 1094 1094 104 104 8110 8110 637 637 False -metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid Taxonomic classification Taxonomy To update https://github.com/steineggerlab/Metabuli Sequence Analysis, Metagenomics metabuli 2024-06-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli 1.0.5 metabuli 1.0.8 Taxonomic classification Taxonomy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation 2020-08-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 Homology-based gene prediction Metagenomics, Gene and protein families 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 312 40 40 0 0 0 0 0 0 0 0 312 312 40 40 False -metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator 2018-03-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 Sequence annotation Genomics, Model organisms, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 980 980 323 323 0 0 0 0 0 0 0 0 980 980 323 323 False -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html Metagenomics metagenomeseq_normalization 2017-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 Sequence visualisation, Statistical calculation Metagenomics, Sequencing 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 556 756 17 21 310 514 35 55 0 0 0 0 866 1270 52 76 False -metanovo metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo 2022-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4471 4471 29 29 0 0 0 0 0 0 0 0 4471 4471 29 29 False -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan 2021-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.1.1 metaphlan 4.1.1 Nucleic acid sequence analysis Metagenomics, Phylogenomics 1 2 4 4 1 2 4 4 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 16629 16648 1183 1187 3983 3983 572 572 4747 4747 278 278 25359 25378 2033 2037 False -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome 2019-04-05 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics 0 6 6 0 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 2730 2831 260 262 0 0 0 0 1540 1540 71 71 4270 4371 331 333 False -metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning 2024-04-11 galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 142 142 32 32 0 0 0 0 379 379 47 47 521 521 79 79 False -metfrag metfrag [Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2019-08-01 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag 2.4.5+galaxy3 metfrag 2.4.5 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 192 192 20 20 0 0 0 0 0 0 0 0 192 192 20 20 False -metfrag-vis metfrag_vis [Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag To update https://github.com/computational-metabolomics/metfrag-galaxy Metabolomics 2020-06-30 computational-metabolomics https://github.com/computational-metabolomics/metfrag-galaxy https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis 2.4.5+galaxy0 metfrag 2.4.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 50 50 14 14 0 0 0 0 0 0 0 0 50 50 14 14 False -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 632 5461 155 453 0 0 0 0 0 0 0 0 632 5461 155 453 False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh 2017-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 14907 18971 638 894 2677 2677 230 230 2313 2313 83 83 19897 23961 951 1207 False -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit 2016-12-20 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -metilene metilene Differential DNA methylation calling To update RNA, Statistics metilene 2015-12-14 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3209 4572 312 442 479 479 79 79 315 315 51 51 4003 5366 442 572 False -mfassignr mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements mfassignr mfassignr MFAssignR Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows Up-to-date https://github.com/RECETOX/MFAssignR Metabolomics MFAssignR 2024-08-08 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr 1.1.1 r-mfassignr 1.1.1 Visualisation Proteomics experiment, Molecular interactions, pathways and networks, Workflows 0 0 9 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 8 8 0 0 0 0 0 0 0 0 10 10 8 8 False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. mg-toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. Data retrieval Metagenomics Up-to-date https://github.com/EBI-Metagenomics/emg-toolkit Metagenomics mg_toolkit 2024-07-12 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit 0.10.4 mg-toolkit 0.10.4 Data retrieval Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -mgf_formatter mgf_formatter Up-to-date mgf_formatter 2014-09-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep 2024-05-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 573 573 3 3 0 0 0 0 0 0 0 0 573 573 3 3 False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsatbed microsatbed Select microsatellites for a bed file To update https://github.com/lmdu/pytrf Sequence Analysis microsatbed 2024-07-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1.3.3 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 228 228 4 4 18 18 1 1 0 0 0 0 246 246 5 5 False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 135 973 50 140 0 0 0 0 135 973 50 140 False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 312 22 87 0 0 0 0 34 312 22 87 False -migmap migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap 2017-09-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 Sequence analysis, Read mapping Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1082 1229 25 33 1153 1376 70 89 0 0 0 0 2235 2605 95 122 False -minced minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1213 1309 115 124 0 0 0 0 0 0 0 0 1213 1309 115 124 False -mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 11 8 8 17 63 6 19 0 0 0 0 26 74 14 27 False -minia minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 Genome assembly Sequence assembly 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7116 7116 256 256 0 0 0 0 278 278 60 60 7394 7394 316 316 False -miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm 2019-06-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 De-novo assembly Genomics, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13357 13479 554 562 8416 8416 448 448 898 898 85 85 22671 22793 1087 1095 False -minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 2018-08-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 Pairwise sequence alignment Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 346530 349075 4323 4419 108535 108535 4075 4075 22331 22331 1166 1166 477396 479941 9564 9660 False -minipolish minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish 2022-10-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 Localised reassembly, Read depth analysis Sequence assembly, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 229 229 32 32 0 0 0 0 0 0 0 0 229 229 32 32 False -miniprot miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis 2023-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1244 1244 86 86 24 24 15 15 0 0 0 0 1268 1268 101 101 False -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda 2015-10-30 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6408 6514 94 99 0 0 0 0 0 0 0 0 6408 6514 94 99 False -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko 2018-04-12 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 False -mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine 2024-03-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 False -mirnature mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature 2022-12-11 iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -misc target_screen, use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics 2024-02-16 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 pandas 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 0 0 0 0 0 0 0 0 6 6 2 2 False -mitobim mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim 2020-12-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1117 1117 116 116 0 0 0 0 295 295 25 25 1412 1412 141 141 False -mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi 2021-05-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1020 1020 176 176 414 414 73 73 277 277 20 20 1711 1711 269 269 False -mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos 2020-02-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 Genome annotation Zoology, Whole genome sequencing 1 1 2 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 191295 191295 1111 1111 42265 42265 320 320 10904 10904 83 83 244464 244464 1514 1514 False -mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures 2022-05-16 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mlst mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst 2016-12-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 Multilocus sequence typing Immunoproteins and antigens 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 13300 13471 1480 1501 6532 6532 1167 1167 10334 11841 1083 1300 30166 31844 3730 3968 False -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff 2019-01-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 331 762 20 34 0 0 0 0 137 137 4 4 468 899 24 38 False -moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs 2019-07-28 iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 339 339 56 56 0 0 0 0 0 0 0 0 339 339 56 56 False -mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite 2018-08-20 nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 119024 119024 628 628 42 42 2 2 36310 36310 191 191 155376 155376 821 821 False -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 False -morpheus morpheus Morpheus MS Search Application morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. Peptide database search Proteomics To update https://cwenger.github.io/Morpheus Proteomics morpheus 2015-10-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 288 morpheus 290 Peptide database search Proteomics 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 105 153 12 19 0 0 0 0 833 833 93 93 938 986 105 112 False -morphological_operations morphological_operations Apply morphological operations to images scipy To update https://github.com/bmcv Imaging morphological_operations 2024-03-08 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations 1.12.0 scipy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mosdepth mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth 2022-12-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1278 1278 87 87 168 168 24 24 102 102 5 5 1548 1548 116 116 False -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur 2018-08-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny 129 129 129 129 129 129 129 129 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 297546 326056 37506 41763 565218 682083 72163 89926 167400 182490 26963 28404 1030164 1190629 136632 160093 False -motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. mOTUs mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. Taxonomic classification Metagenomics Up-to-date https://github.com/motu-tool/mOTUs Metagenomics motus 2024-09-06 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus 3.1.0 motus 3.1.0 Taxonomic classification Metagenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc 2017-08-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 71 76 9 9 0 0 0 0 0 0 0 0 71 76 9 9 False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep 2022-03-31 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 13 13 3 3 0 0 0 0 0 0 0 0 13 13 3 3 False -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes 2015-12-04 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening To update https://github.com/matchms/ms2deepscore Metabolomics ms2deepscore 2024-08-15 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore 2.0.0 ms2deepscore 2.2.0 Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop 2022-03-15 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msPurity mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data Up-to-date https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-05-24 computational-metabolomics https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity 1.28.0 bioconductor-mspurity 1.28.0 0 0 10 11 0 0 10 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 848 848 91 91 0 0 0 0 0 0 0 0 848 848 91 91 False -msaboot msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot 2018-02-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 864 929 91 101 1100 1100 175 175 0 0 0 0 1964 2029 266 276 False -msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert 2019-02-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 Filtering, Formatting Proteomics, Proteomics experiment 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20749 22184 455 469 1239 1239 71 71 2666 2666 53 53 24654 26089 579 593 False -msgfplus msgfplus MSGF+ To update Proteomics msgfplus 2017-01-12 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 473 529 33 43 0 0 0 0 0 0 0 0 473 529 33 43 False -msmetaenhancer msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics 2022-04-22 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 10 10 0 0 0 0 48 48 1 1 251 251 11 11 False -msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor 2019-10-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 110 110 11 11 0 0 0 0 0 0 0 0 110 110 11 11 False -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics 2022-05-05 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.27.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msp_split msp_split [Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data To update https://github.com/computational-metabolomics/mspurity-galaxy Metabolomics 2019-09-24 tomnl https://github.com/computational-metabolomics/mspurity-galaxy https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split 0.0.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -msstats msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics 2020-07-25 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2353 2353 559 559 1122 1122 211 211 1091 1091 35 35 4566 4566 805 805 False -msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt 2021-02-26 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 795 795 104 104 0 0 0 0 461 461 12 12 1256 1256 116 116 False -mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq 2020-06-23 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 275 275 38 38 0 0 0 0 0 0 0 0 275 275 38 38 False -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps 2017-03-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 485 871 159 298 0 0 0 0 485 871 159 298 False -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 False -multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc 2020-04-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.24.1 multiqc 1.25.1 Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 182221 192389 19343 20494 163961 182413 26449 29758 40663 41855 5974 6157 386845 416657 51766 56409 False -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 883 921 199 211 730 730 199 199 136 202 34 49 1749 1853 432 459 False -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 2018-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 Multiple sequence alignment Sequence analysis, Human genetics 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 21587 22119 1940 2033 29284 29284 3626 3626 8194 8194 545 545 59065 59597 6111 6204 False -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 False -mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 44 49 5 5 81 417 23 118 0 0 0 0 125 466 28 123 False -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns 2020-10-19 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe 2017-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser 2018-09-28 nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite 2015-06-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 Conversion, Peptide database search Proteomics, Biological databases 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 854 860 110 111 79 79 15 15 274 274 13 13 1207 1213 138 139 False -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch 2023-10-21 iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 0 0 0 0 0 0 0 0 9 9 5 5 False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics 2023-01-12 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML To update https://rdrr.io/bioc/mzR/ Metabolomics mzxmlshaper 2024-09-20 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 1.0.0+galaxy0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis 2022-04-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 204 204 75 75 0 0 0 0 204 204 75 75 False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites 0 1 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 839 839 12 12 0 0 0 0 269 269 5 5 1108 1108 17 17 False -nanoplot nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot 2018-09-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.43.0 nanoplot 1.43.0 Scatter plot plotting, Box-Whisker plot plotting Genomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 99052 100009 5671 5755 40386 40386 3371 3371 17919 17919 2188 2188 157357 158314 11230 11314 False -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish 2018-06-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 0 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 9284 9694 215 229 0 0 0 0 2358 2358 49 49 11642 12052 264 278 False -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1091 1091 44 44 0 0 0 0 0 0 0 0 1091 1091 44 44 False -nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq 2017-02-21 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 40 1 1 0 0 0 0 0 0 0 0 36 40 1 1 False -ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download 2019-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6873 6873 1664 1664 17651 17651 4513 4513 6228 6228 972 972 30752 30752 7149 7149 False -ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus 2020-09-08 devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python 16 16 16 16 16 16 16 16 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 391141 443752 9760 10546 306361 350178 11767 13684 227235 244814 3192 3617 924737 1038744 24719 27847 False -ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.20.0 ncbi-datasets-cli Data handling, Sequence database search, Data retrieval Biological databases 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4417 4417 1024 1024 6940 6940 2275 2275 1 1 1 1 11358 11358 3300 3300 False -ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) To update https://github.com/ncbi/egapx Genome annotation ncbi_egapx 2024-08-19 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 0.2-alpha 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 6 6 0 0 0 0 15 15 6 6 False -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct 2022-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 22.4 entrez-direct 22.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 3 0 2 False -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils 2020-08-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 4 0 0 4 0 0 0 2 0 0 0 0 0 0 0 7 7 0 2794 3191 533 664 0 0 0 0 0 0 0 0 2794 3191 533 664 False -ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor 2024-02-23 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 842 842 93 93 0 0 0 0 842 842 93 93 False -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx 2023-11-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.4 ncbi-fcs-gx 0.5.4 Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 125 125 26 26 2489 2489 139 139 0 0 0 0 2614 2614 165 165 False -necat necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat 2021-11-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 De-novo assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 790 790 160 160 0 0 0 0 0 0 0 0 790 790 160 160 False -netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr 2022-08-24 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 6 6 0 0 0 0 0 0 0 0 12 12 6 6 False -newick_utils newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils 2018-10-01 iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 Phylogeny, Genomics, Computer science 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 33637 34195 1113 1172 16257 16257 1816 1816 7582 7582 899 899 57476 58034 3828 3887 False -nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis 2021-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 Methylation analysis, Variant calling Genomics, Cladistics 1 1 2 2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 0 4411 4411 396 396 9708 9708 279 279 2099 2099 212 212 16218 16218 887 887 False -nextdenovo nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo 2023-02-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 De-novo assembly, Genome assembly Sequencing, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 391 391 158 158 0 0 0 0 0 0 0 0 391 391 158 158 False -ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr 2020-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1403 1403 49 49 0 0 0 0 0 0 0 0 1403 1403 49 49 False -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM 2015-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 24611 29662 633 716 15523 21395 740 1128 7751 8972 125 145 47885 60029 1498 1989 False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus 2013-09-10 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 49 49 5 5 0 0 0 0 0 0 0 0 49 49 5 5 False -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation 2021-01-21 marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing 2019-07-29 marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 142 142 8 8 0 0 0 0 335 341 9 9 477 483 17 17 False -nonpareil nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil 2017-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.5.5 Operation 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 143 13 15 148 148 20 20 0 0 0 0 255 291 33 35 False -normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization 2019-07-30 marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 152 162 39 40 0 0 0 0 233 236 12 12 385 398 51 52 False -novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty 2020-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 7780 7780 337 337 1 1 1 1 2323 2323 99 99 10104 10104 437 437 False -nucleosome_prediction Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction 2016-09-27 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 118 863 19 26 0 0 0 0 0 0 0 0 118 863 19 26 False -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering 2015-12-19 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 391 486 5 11 0 0 0 0 0 0 0 0 391 486 5 11 False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases 2017-10-15 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -obisindicators obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology 2022-11-04 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base 1 0 2 1 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 352 352 42 42 8 8 6 6 0 0 0 0 360 360 48 48 False -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools 2017-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing 0 10 10 10 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 37598 37598 1277 1277 0 0 0 0 3862 3862 280 280 41460 41460 1557 1557 False -ocean argo_getdata, divand_full_analysis Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology 2023-11-17 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 julia 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 False -ococo ococo Variant detection of SNVs To update https://github.com/karel-brinda/ococo Variant Analysis ococo 2017-12-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1850 1963 79 93 1370 1370 194 194 0 0 0 0 3220 3333 273 287 False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.9.0 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 98 6 6 0 0 0 0 0 0 0 0 98 98 6 6 False -ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology 2024-03-12 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 57 4 4 0 0 0 0 0 0 0 0 57 57 4 4 False -omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark 2023-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 158 158 12 12 0 0 0 0 0 0 0 0 158 158 12 12 False -omero omero_import, omero_metadata_import, omero_roi_import Import images, region of interest, metadata into an OMERO.server using omero-py omero omero OMERO Client-server Java software for visualisation, management and analysis of biological microscope images. Image analysis Imaging, Data visualisation To update https://github.com/ome/omero-py/ Imaging omero_upload 2024-07-29 ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero 5.18.0 omero-py 5.11.1 Image analysis Imaging, Data visualisation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables 2023-06-23 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids 2023-12-22 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.2.0 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images 2024-05-21 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements 2023-03-24 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20240614 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api 2020-06-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 3051 3051 87 87 0 0 0 0 0 0 0 0 3051 3051 87 87 False -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit 2017-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 0 0 17 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 582 663 68 69 0 0 0 0 0 0 0 0 582 663 68 69 False -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv 2021-10-28 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm 2022-03-25 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 491 491 52 52 0 0 0 0 0 0 0 0 491 491 52 52 False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms 2024-04-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 3.1 openms 3.2.0 8 34 144 0 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 32169 108654 3316 4889 50 50 15 15 940 940 245 245 33159 109644 3576 5149 False -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.2.0 7 34 135 0 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 135 134 0 31121 108907 3369 5029 50 50 15 15 933 933 242 242 32104 109890 3626 5286 False -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe 2022-10-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -optitype optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype 2021-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 500 500 45 45 0 0 0 0 0 0 0 0 500 500 45 45 False -orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy 2022-04-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 897 897 99 99 1792 1792 239 239 0 0 0 0 2689 2689 338 338 False -orientationpy orientationpy Compute image orientation orientationj Up-to-date https://github.com/bmcv Imaging orientationpy 2024-03-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy 0.2.0.4 orientationpy 0.2.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 3.0.1b1 Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 2018 2018 419 419 0 0 0 0 438 438 58 58 2456 2456 477 477 False -overlay_images ip_overlay_images Overlay two images galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images 2022-02-26 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images 0.0.4 scikit-image Image analysis Imaging, Bioinformatics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 149 149 31 31 0 0 0 0 18 18 1 1 167 167 32 32 False -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader Data Source packaged_annotation_loader 2022-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol 2018-10-04 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 282 295 32 33 420 420 8 8 0 0 0 0 702 715 40 41 False -pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). Clustering Phylogenetics, Sequence analysis Up-to-date https://github.com/BioinformaticsPlatformWIV-ISP/PACU Sequence Analysis, Phylogenetics pacu 2024-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu 0.0.5 pacu_snp 0.0.5 Clustering Phylogenetics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools 2024-03-26 iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 5 0 5 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 196 196 16 16 19 19 14 14 0 0 0 0 215 215 30 30 False -pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window 2019-05-20 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 261 275 12 12 63 63 22 22 0 0 0 0 324 338 34 34 False -pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin 2021-04-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 Tree-based sequence alignment, Variant classification Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin 2020-05-01 nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 7457 7457 508 508 8518 8518 377 377 2760 2760 259 259 18735 18735 1144 1144 False -paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer 2016-12-02 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 322 349 24 29 0 0 0 0 0 0 0 0 322 349 24 29 False -parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast 2022-05-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 65 65 288 288 62 62 110 110 20 20 601 601 147 147 False -partialr_square partialRsq Compute partial R square To update Statistics partialr_square 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 142 8 42 0 0 0 0 55 142 8 42 False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 False -pathview pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview 2019-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6204 6211 1261 1261 6667 6667 1143 1143 1160 1160 189 189 14031 14038 2593 2593 False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher 2018-06-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 174 244 65 76 0 0 0 0 0 0 0 0 174 244 65 76 False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist 2019-12-14 nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp 2022-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 Variant calling Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 2022-03-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.14.99 pbmm2 1.14.99 Pairwise sequence alignment, Sorting Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 70 17 17 0 0 0 0 0 0 0 0 70 70 17 17 False -pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 58 22 22 109 109 19 19 0 0 0 0 167 167 41 41 False -pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram 2016-06-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.2 openjdk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5505 5505 510 510 7932 8582 811 909 736 736 119 119 14173 14823 1440 1538 False -peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu 2018-02-14 rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2807 3337 178 196 0 0 0 0 0 0 0 0 2807 3337 178 196 False -peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla 2024-02-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 9 9 0 0 0 0 0 0 0 0 18 18 9 9 False -pear iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date https://cme.h-its.org/exelixis/web/software/pear/ Fastq Manipulation pear 2015-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 Sequence merging Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 6269 6866 260 292 5530 20068 467 1664 5647 8471 198 300 17446 35405 925 2256 False -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 2 0 2 False -pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer 2017-12-19 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 506 511 54 55 21 21 12 12 163 163 8 8 690 695 74 75 False -pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery 2020-01-22 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7047 7047 76 76 0 0 0 0 0 0 0 0 7047 7047 76 76 False -pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 2022-10-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 0 1 3 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1222 1222 28 28 0 0 0 0 0 0 0 0 1222 1222 28 28 False -peptide_genomic_coordinate peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate 2019-03-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 472 472 56 56 16 16 10 10 149 149 5 5 637 637 71 71 False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker 2021-04-02 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.11 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 2 0 11986 17898 1046 1153 1314 1314 389 389 3034 3034 118 118 16334 22246 1553 1660 False -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics 2021-11-03 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.1 0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator 2017-03-03 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.7.1 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 338 378 15 16 0 0 0 0 1059 1059 13 13 1397 1437 28 29 False -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -permutate_axis ip_permutate_axis Permutates axes galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis 0.2-2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 42 1 2 0 0 0 0 0 0 0 0 36 42 1 2 False -pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan 2023-02-02 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 Protein sequence analysis Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 773 773 60 60 495 495 72 72 246 246 17 17 1514 1514 149 149 False -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools 2017-09-28 bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat 2022-01-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 109 109 29 29 250 250 84 84 0 0 0 0 359 359 113 113 False -pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka 2023-02-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 5462 5462 334 334 0 0 0 0 309 309 52 52 5771 5771 386 386 False -phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq 2022-03-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics 4 1 4 4 4 1 4 4 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1199 1199 193 193 0 0 0 0 6 6 1 1 1205 1205 194 194 False -phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml 2019-05-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 Phylogenetics, Bioinformatics, Phylogenetics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1975 2034 246 258 0 0 0 0 553 564 140 144 2528 2598 386 402 False -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit 2022-09-28 workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.4.0 physiofit 3.4.0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date physiofit.readthedocs.io Metabolomics physiofit_manager 2022-11-03 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools 2017-04-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard 2019-05-30 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.3.0 Formatting Sequencing 31 31 31 31 31 31 31 31 0 0 0 0 0 0 0 0 31 4 31 0 0 31 0 0 0 31 0 0 0 0 0 0 31 31 31 0 386934 399039 11024 11956 366646 589980 32000 57111 56622 62258 2845 3398 810202 1051277 45869 72465 False -pick_value pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value 2023-01-23 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1607 1607 41 41 490 490 53 53 127 127 4 4 2224 2224 98 98 False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust 2017-07-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing 0 6 5 6 0 6 5 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 867 1128 144 165 0 0 0 0 2106 2106 121 121 2973 3234 265 286 False -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Up-to-date https://github.com/picrust/picrust2/wiki Metagenomics picrust2 2021-11-07 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.3 picrust2 2.5.3 Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2532 2532 382 382 1 1 1 1 1311 1311 83 83 3844 3844 466 466 False -pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval 2015-03-06 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 613 640 48 54 1381 7804 201 1552 756 815 22 30 2750 9259 271 1636 False -pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3639 3774 414 461 9754 52522 1247 4531 1893 2433 191 318 15286 58729 1852 5310 False -pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update https://github.com/broadinstitute/pilon/wiki Variant Analysis pilon 2016-08-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 Sequence assembly, Analysis Assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9045 9458 1115 1144 7989 7989 1070 1070 3945 4137 726 741 20979 21584 2911 2955 False -pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel 2021-09-29 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign 2019-08-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1245 1245 231 231 9046 9046 630 630 0 0 0 0 10291 10291 861 861 False -pipmir pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir 2016-11-25 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 283 42 45 0 0 0 0 0 0 0 0 238 283 42 45 False -piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha 2015-07-02 rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1408 2068 94 119 0 0 0 0 0 0 0 0 1408 2068 94 119 False -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 False -plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy To update https://github.com/bmcv Imaging plantseg 2024-06-19 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg 1.8.1 plant-seg Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 Sequence analysis Metagenomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37086 37272 711 734 6346 6346 583 583 3065 3065 61 61 46497 46683 1355 1378 False -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler 2016-11-07 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plasmidfinder plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder 2022-09-19 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14652 14652 251 251 0 0 0 0 101 101 18 18 14753 14753 269 269 False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades 2016-06-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 4.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink 2020-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 Genetic variation analysis GWAS study 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 851 851 127 127 249 249 43 43 0 0 0 0 1100 1100 170 170 False -plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 77 19 25 153 886 38 343 142 155 8 10 360 1118 65 378 False -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap 2017-07-04 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots 2018-10-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.4 galaxy-ml 0.10.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1342 1472 184 197 902 902 156 156 630 630 24 24 2874 3004 364 377 False -plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot 2018-09-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 408 664 91 122 627 627 118 118 605 605 26 26 1640 1896 235 266 False -plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots 2018-10-30 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 764 879 213 237 304 304 95 95 193 193 26 26 1261 1376 334 358 False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr 2019-10-01 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat 2020-03-24 nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -points2labelimage ip_points_to_label Points to label image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage 2018-11-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage 0.4 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 33 2 2 0 0 0 0 0 0 0 0 33 33 2 2 False -points_association_nn ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn 2021-07-22 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn 0.0.3-2 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4 4 0 0 0 0 0 0 0 0 29 29 4 4 False -poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 112 120 16 16 4 562 1 140 320 347 7 8 436 1029 24 164 False -polypolish polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish 2022-09-22 iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 731 731 86 86 0 0 0 0 42 42 4 4 773 773 90 90 False -porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop 2018-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 262015 262852 2627 2711 83623 83623 1918 1918 52558 52558 1037 1037 398196 399033 5582 5666 False -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation 2017-12-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 Nucleic acid sequence analysis DNA, Sequencing 13 13 13 0 13 13 13 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 19942 20587 1055 1245 33619 40808 2183 2594 9261 9261 365 365 62822 70656 3603 4204 False -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment 2016-11-04 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment 2016-11-07 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto 2017-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 Nucleic acid sequence analysis Sequencing, DNA, Immunology 11 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63244 65177 1392 1599 0 0 0 0 63244 65177 1392 1599 False -pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext 2021-04-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 3 2 3 0 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3463 3463 538 538 1853 1853 256 256 1097 1097 70 70 6413 6413 864 864 False -principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9788 10032 207 244 3072 8054 607 1488 0 0 0 0 12860 18086 814 1732 False -prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq 2016-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10152 10626 253 281 10581 10581 1240 1240 0 0 0 0 20733 21207 1493 1521 False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage 2017-09-22 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal 2024-03-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 Genome annotation Genomics, Sequence analysis 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1902 1902 167 167 0 0 0 0 0 0 0 0 1902 1902 167 167 False -progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update http://darlinglab.org/mauve/user-guide/progressivemauve.html Sequence Analysis progressivemauve 2015-05-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2064 2173 678 695 2900 2900 1034 1034 0 0 0 0 4964 5073 1712 1729 False -projective_transformation ip_projective_transformation Projective transformation galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation 0.1.2 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 86 4 6 0 0 0 0 0 0 0 0 40 86 4 6 False -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points 0.1.1 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20858 21444 14 18 0 0 0 0 0 0 0 0 20858 21444 14 18 False -prokka prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka 2016-10-10 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 Coding region prediction, Genome annotation Genomics, Model organisms, Virology 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 1 1 1 0 464359 476554 7475 7721 313285 331256 11243 12384 131211 141875 4358 4947 908855 949685 23076 25052 False -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer 2019-12-14 nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber 2022-05-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.6 prot-scriber 0.1.6 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 7 7 0 0 0 0 0 0 0 0 10 10 7 7 False -protease_prediction eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction 2016-03-13 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 129 155 15 21 0 0 0 0 0 0 0 0 129 155 15 21 False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp 2017-08-30 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 11743 12752 1137 1278 2 2 1 1 0 0 0 0 11745 12754 1138 1279 False -protein_properties bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties 2015-06-07 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 465 638 81 100 0 0 0 0 0 0 0 0 465 638 81 100 False -proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho 2020-10-02 iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.2 Sequence clustering, Sequence analysis Comparative genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3962 3962 501 501 0 0 0 0 0 0 0 0 3962 3962 501 501 False -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 366 366 4 4 0 0 0 0 0 0 0 0 366 366 4 4 False -proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification 2021-09-16 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 8 8 0 0 0 0 0 0 0 0 16 16 8 8 False -proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification 2021-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 4 4 0 0 0 0 0 0 0 0 6 6 4 4 False -proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite 2021-06-30 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 721 721 8 8 0 0 0 0 0 0 0 0 721 721 8 8 False -proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb 2021-07-04 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 96 96 12 12 0 0 0 0 0 0 0 0 96 96 12 12 False -proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching 2021-07-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 686 686 5 5 0 0 0 0 0 0 0 0 686 686 5 5 False -proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 6 6 0 0 0 0 0 0 0 0 89 89 6 6 False -proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 604 604 4 4 0 0 0 0 0 0 0 0 604 604 4 4 False -proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics 2021-07-09 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 694 694 6 6 0 0 0 0 0 0 0 0 694 694 6 6 False -proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram 2021-05-17 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 1 1 0 0 0 0 0 0 0 0 15 15 1 1 False -protxml_to_xls protxml_to_xls To update protxml_to_xls 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome 2018-04-06 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam 2017-10-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_eval psm_eval To update psm_eval 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -psm_validation psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation 2020-10-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 4 4 0 0 0 0 0 0 0 0 20 20 4 4 False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps 2019-10-04 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.3.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 333 502 62 62 0 0 0 0 0 0 0 0 333 502 62 62 False -pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip 2018-04-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1319 1507 81 92 0 0 0 0 0 0 0 0 1319 1507 81 92 False -purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups 2021-02-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 Genome assembly, Read binning, Scaffolding Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17782 17782 287 287 853 853 65 65 2224 2224 65 65 20859 20859 417 417 False -pycoqc pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc 2021-03-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 22742 22742 557 557 2159 2159 716 716 776 776 448 448 25677 25677 1721 1721 False -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client 2022-10-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2716 2716 104 104 134 134 43 43 40 40 1 1 2890 2890 148 148 False -pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks 2020-03-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 Visualisation, Formatting Model organisms, Imaging, Workflows 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12858 13232 986 996 8092 8092 943 943 3238 3238 124 124 24188 24562 2053 2063 False -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 0 5 6 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 2626 2626 150 150 0 0 0 0 609 609 9 9 3235 3235 159 159 False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search 2022-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.2 Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 163 163 35 35 0 0 0 0 0 0 0 0 163 163 35 35 False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics 2021-01-15 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.5 Protein identification Proteomics, Proteomics experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 4 4 0 0 0 0 0 0 0 0 92 92 4 4 False -pyvo_integration astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy To update Data Source astronomicalarchivestool 2023-08-26 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0.10.0 astropy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 53 53 6 6 0 0 0 0 0 0 0 0 53 53 6 6 False -qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS 2023-10-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11246 11246 13 13 0 0 0 0 0 0 0 0 11246 11246 13 13 False -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_core, qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-01-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 2092 2342 209 238 0 0 0 0 2 2 1 1 2094 2344 210 239 False -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime 2017-06-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics 0 0 32 32 0 0 32 32 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 31825 34677 3375 3785 1 1 1 1 14 14 4 4 31840 34692 3380 3790 False -qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz 2022-10-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 8 8 0 0 0 0 0 0 0 0 17 17 8 8 False -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis 2020-10-07 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 False -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.13.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98 724 35 62 0 0 0 0 98 724 35 62 False -quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp 2018-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 197 241 17 22 0 0 0 0 0 0 0 0 197 241 17 22 False -quantwiz_iq quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq 2020-01-21 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 32 3 3 0 0 0 0 0 0 0 0 32 32 3 3 False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools 2018-07-06 nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 0 12 0 12 0 12 0 12 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13483 13483 434 434 13483 13483 434 434 False -quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast 2018-02-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 Visualisation, Sequence assembly validation Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 67737 69738 7787 7971 51925 56602 9692 10646 32003 34145 3890 4127 151665 160485 21369 22744 False -query query Execute an SQL statement on a set of tables To update Text Manipulation query 2020-12-09 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -query_impc query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc 2023-10-11 iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 0 0 0 0 0 0 0 0 3 3 2 2 False -query_tabular filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular Text Manipulation 2017-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.1 python 3 3 3 1 3 3 3 1 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 130124 135361 1265 1305 11135 11135 922 922 5939 5939 153 153 147198 152435 2340 2380 False -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge 2022-07-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -qupath_roi_splitter qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter 2023-04-12 galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.3.2 geojson 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 172 172 9 9 0 0 0 0 0 0 0 0 172 172 9 9 False -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon 2018-06-11 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 27113 27315 839 850 9089 9089 475 475 5452 5452 171 171 41654 41856 1485 1496 False -ragtag ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag 2021-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 Genome assembly Sequence assembly 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4844 4844 480 480 0 0 0 0 7 7 3 3 4851 4851 483 483 False -ramclustr ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics 2023-05-31 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 58 58 22 22 29 29 14 14 344 344 4 4 431 431 40 40 False -rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj 2020-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 Phylogeny 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 339 339 30 30 1737 1737 256 256 6 6 1 1 2082 2082 287 287 False -rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa 2024-02-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 2.0.0 rasusa 2.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 9 9 0 0 0 0 0 0 0 0 42 42 9 9 False -raven raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly 2020-11-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9477 9477 438 438 0 0 0 0 10585 10585 182 182 20062 20062 620 620 False -rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools 2019-02-28 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 179 32 33 0 0 0 0 414 414 13 13 580 593 45 46 False -raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml 2015-11-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 Sequence analysis Phylogenetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10905 10905 966 966 5100 5114 587 587 4955 6094 765 892 20960 22113 2318 2445 False -rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis To update https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench 2023-12-03 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 1.0.1 RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 90 6 6 0 0 0 0 0 0 0 0 90 90 6 6 False -rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas 2017-04-13 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 860 1257 88 98 0 0 0 0 0 0 0 0 860 1257 88 98 False -rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 Sequencing error detection RNA, RNA-Seq 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 655 655 57 57 0 0 0 0 0 0 0 0 655 655 57 57 False -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 49 191 5 46 0 0 0 0 49 191 5 46 False -rcx-tk rcx-tk Tools to process metadata or alkane files. To update https://github.com/RECETOX/rcx-tk Metabolomics rcx_tk 2024-08-01 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock 2016-12-14 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep 2022-01-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 Filtering, Genome alignment Pathology, Genomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3710 3710 80 80 7 7 6 6 0 0 0 0 3717 3717 86 86 False -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago 2015-12-09 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -recentrifuge recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge 2022-05-04 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.15.0 recentrifuge 1.15.0 Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 472 472 92 92 32 32 13 13 6 6 4 4 510 510 109 109 False -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms 2023-05-18 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.13.3 r-recetox-aplcms 0.13.3 Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics 0 8 8 8 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 862 862 12 12 0 0 0 0 48 48 1 1 910 910 13 13 False -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics 2022-12-02 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 Annotation Metabolomics 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 4 4 0 0 0 0 0 0 0 0 47 47 4 4 False -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics 2021-07-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 93 93 2 2 93 93 2 2 False -red red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red 2022-09-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 859 859 203 203 305 305 142 142 227 227 58 58 1391 1391 403 403 False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher 2018-01-31 nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 428 428 35 35 141 141 42 42 0 0 0 0 569 569 77 77 False -regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace 2017-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 78648 78834 1144 1156 18063 18063 870 870 4455 6051 194 289 101166 102948 2208 2315 False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology 2019-06-18 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv 0 0 7 7 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 7 0 438 542 128 157 0 0 0 0 0 0 0 0 438 542 128 157 False -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex 2023-11-21 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 2 2 0 0 0 0 0 0 0 0 18 18 2 2 False -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 148572 169964 3525 3682 36694 113826 3910 8163 9713 10577 1475 1598 194979 294367 8910 13443 False -remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 44 6 7 0 0 0 0 0 0 0 0 39 44 6 7 False -rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature 2024-05-13 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -repeat_channels repeat_channels Convert single-channel to multi-channel image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging repeat_channels 2024-04-25 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels 1.26.4 numpy Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 1 1 0 0 0 0 0 0 0 0 5 5 1 1 False -repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.0.9_p2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 2023-11-01 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 38 38 0 0 0 0 0 0 0 0 95 95 38 38 False -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker 2018-04-30 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.0.9_p2 Genome annotation Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5998 5998 810 810 7618 7618 803 803 3135 3135 292 292 16751 16751 1905 1905 False -repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler 2021-08-26 csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7963 7963 413 413 1485 1485 220 220 8402 8402 168 168 17850 17850 801 801 False -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 False -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file 2017-02-24 bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 577184 577312 463 492 43900 44233 283 373 2190 2190 112 112 623274 623735 858 977 False -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names 2017-05-18 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 514 573 69 83 0 0 0 0 0 0 0 0 514 573 69 83 False -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 2015-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 415 721 128 219 0 0 0 0 415 721 128 219 False -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 3543 3619 108 111 536 536 157 157 0 0 0 0 4079 4155 265 268 False -resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window 2016-01-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 86 8 9 138 216 30 57 0 0 0 0 213 302 38 66 False -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics 2020-09-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -retrieve_bold retrieve_bold Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers To update https://anaconda.org/conda-forge/r-bold Ecology retrieve_bold 2024-06-21 ecology https://github.com/wpearman1996/MARES_database_pipeline/tree/master https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold 1.3.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam 2019-04-17 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.21 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 11 11 520 520 31 31 0 0 0 0 560 560 42 42 False -revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer 2024-03-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 Structural variation detection Molecular evolution, Phylogeny 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2444 2444 52 52 0 0 0 0 0 0 0 0 2444 2444 52 52 False -rfove rfove Perform segmentation region-based fitting of overlapping ellipses rfove rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove 2023-11-12 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove 2023.11.12 Image analysis Cell biology, Biomedical science, Imaging 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 7 7 0 0 0 0 0 0 0 0 15 15 7 7 False -rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca 2020-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 6 6 77 77 35 35 0 0 0 0 121 121 41 41 False -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 False -riassigner riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics 2021-08-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation 1 2 2 1 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 19 19 15 15 4 4 1 1 1 1 62 62 24 24 False -ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper 2016-03-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 Gene expression profiling Functional genomics 0 0 3 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 661 681 78 78 0 0 0 0 0 0 0 0 661 681 78 78 False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 False -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank 2021-02-25 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 48 48 1 1 48 48 1 1 False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 173 40 49 0 0 0 0 0 0 0 0 137 173 40 49 False -rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 90 196 9 11 0 0 0 0 0 0 0 0 90 196 9 11 False -rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode 2015-06-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 878 1363 29 35 0 0 0 0 0 0 0 0 878 1363 29 35 False -rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender 2016-05-31 rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1024 1077 18 21 0 0 0 0 0 0 0 0 1024 1077 18 21 False -rnaformer infer_rnaformer RNAformer: RNA secondary structure prediction To update https://github.com/automl/RNAformer RNA rnaformer 2024-07-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer 1.0.0 rnaformer 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 6 6 0 0 0 0 0 0 0 0 26 26 6 6 False -rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien 2017-03-07 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 33 10 14 0 0 0 0 0 0 0 0 23 33 10 14 False -rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast 2023-06-03 iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.3.0 rnaquast 2.3.0 De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1522 1522 254 254 372 372 75 75 5 5 1 1 1899 1899 330 330 False -rnasnp rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp 2016-11-24 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 89 14 18 0 0 0 0 0 0 0 0 65 89 14 18 False -rnaz rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz 2016-10-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 0 1156 43309 93 121 0 0 0 0 0 0 0 0 1156 43309 93 121 False -roary roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary 2017-06-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 Genome assembly DNA, Genomics, Mapping 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15196 15685 1459 1501 12188 12188 1768 1768 4881 5539 518 555 32265 33412 3745 3824 False -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor 2023-01-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths 2022-10-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign 2022-03-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba 2022-01-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools 2022-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser 2022-06-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps 2016-01-29 earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 False -sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish 2015-09-05 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3628 4168 165 199 8399 14473 573 1147 2710 3000 151 175 14737 21641 889 1521 False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 False -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x 2019-11-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 682 682 172 172 322 322 74 74 3 3 3 3 1007 1007 249 249 False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa 2021-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 463 463 119 119 1038 1038 87 87 410 410 24 24 1911 1911 230 230 False -sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1155 1251 57 63 2264 18187 189 1748 525 590 10 17 3944 20028 256 1828 False -sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter 2013-08-26 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python 1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 278 12 26 3554 76029 450 6346 229 345 16 29 3879 76652 478 6401 False -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba 2020-05-19 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 684 684 17 17 684 684 17 17 False -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! Up-to-date https://github.com/biod/sambamba SAM sambamba 2016-06-23 bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 1.0.1 sambamba 1.0.1 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 297 297 51 51 0 0 0 0 0 0 0 0 297 297 51 51 False -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping Up-to-date https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster 2016-12-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.26 samblaster 0.1.26 Split read mapping DNA, Sequencing, Mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs 2015-08-26 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3421 3859 340 382 883 883 109 109 1138 1138 15 15 5442 5880 464 506 False -samtools To update https://github.com/samtools/samtools SAM 2021-01-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.20 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad 2014-04-14 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -samtools_depth samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth 2014-11-19 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6485 6549 720 726 10127 10127 1518 1518 238 238 37 37 16850 16914 2275 2281 False -samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats 2013-11-11 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.21 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 52099 55110 4053 4497 73194 108684 6930 9936 14771 15714 1222 1419 140064 179508 12205 15852 False -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa 2020-12-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.2 sansa 0.2.2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 138 138 36 36 0 0 0 0 0 0 0 0 138 138 36 36 False -sarscov2formatter sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 174 16 16 399 399 29 29 0 0 0 0 573 573 45 45 False -sarscov2summary sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary 2020-05-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 140 140 5 5 253 253 6 6 0 0 0 0 393 393 11 11 False -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol 2022-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 False -scaffold scaffold, scaffold_export To update scaffold 2015-01-24 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -scale_image ip_scale_image Scale image scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image 2018-12-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image 0.18.3 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 477 520 13 16 0 0 0 0 0 0 0 0 477 520 13 16 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 False -scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1234 1752 179 261 680 9223 231 1927 0 49 0 18 1914 11024 410 2206 False -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 False -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio 2016-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1503 1955 283 402 0 0 0 0 1504 1956 284 403 False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 False -scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary 2021-03-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 901 901 90 90 0 0 0 0 0 0 0 0 901 901 90 90 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 False -scripting singularity_scriptrunner suite_scripting To update https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ Text Manipulation scripting tools 2023-07-29 mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors 2024-03-29 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr 2020-02-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5106 5106 116 116 6419 6419 241 241 0 0 0 0 11525 11525 357 357 False -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 281 2284 10 53 0 0 0 0 0 0 0 0 281 2284 10 53 False -segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign 2024-04-18 richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.7 segalign-galaxy 0.1.2.7 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 252 252 47 47 0 0 0 0 252 252 47 47 False -segemehl segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl 2015-02-28 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1095 1306 98 113 0 0 0 0 0 0 0 0 1095 1306 98 113 False -segmetrics ip_segmetrics Image segmentation and object detection performance measures segmetrics segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis To update https://github.com/bmcv Imaging segmetrics 2022-10-07 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics 1.4 segmetrics 1.5 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 2 2 0 0 0 0 0 0 0 0 7 7 2 2 False -selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa 2017-03-11 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 305 463 43 50 0 0 0 0 0 0 0 0 305 463 43 50 False -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper 2022-06-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin 2022-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly 0 0 6 1 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 931 931 93 93 0 0 0 0 0 0 0 0 931 931 93 93 False -seq2hla seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla 2020-02-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 Read mapping, Genetic variation analysis Transcriptomics, Mapping 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 342 40 40 0 0 0 0 0 0 0 0 342 342 40 40 False -seq_composition seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition 2014-08-12 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1053 1186 137 195 680 680 206 206 0 0 0 0 1733 1866 343 401 False -seq_filter_by_id seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id 2016-05-17 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 30300 32553 732 799 21726 31891 619 621 2886 2886 144 144 54912 67330 1495 1564 False -seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping 2015-04-29 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4322 4714 180 205 0 0 0 0 0 0 0 0 4322 4714 180 205 False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length 2018-05-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip 2015-04-28 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename 2014-12-02 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id 2015-04-24 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2196 3529 260 289 2196 3529 260 289 False -seqcomplexity seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis 2022-06-07 iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 70 70 19 19 109 109 47 47 0 0 0 0 179 179 66 66 False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit 2022-06-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis 0 2 5 3 0 2 5 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3364 3364 247 247 0 0 0 0 244 244 33 33 3608 3608 280 280 False -seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep 2024-01-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2424 2424 102 102 0 0 0 0 0 0 0 0 2424 2424 102 102 False -seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 2023-11-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4182 4182 42 42 0 0 0 0 0 0 0 0 4182 4182 42 42 False -seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk 2017-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 Data handling, Sequence file editing 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 14 0 14 0 0 14 0 0 0 15 0 0 0 0 0 0 14 14 14 14 72816 73514 2210 2300 102777 107831 2313 2669 154613 154613 682 682 330206 335958 5205 5651 False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml 2017-09-19 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter 2017-09-04 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -seqwish seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis 2020-04-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 271 271 2 2 0 0 0 0 0 0 0 0 271 271 2 2 False -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sgwb sgwb_astro_tool SGWB To update Astronomy sgwb_astro_tool 2024-04-17 astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0.0.1+galaxy0 ipython 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 0 0 0 0 0 0 0 0 5 5 2 2 False -shasta shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta 2020-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.13.0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 913 913 308 308 0 0 0 0 568 568 73 73 1481 1481 381 381 False -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes 2019-03-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 64 4 4 0 0 0 0 0 0 0 0 54 64 4 4 False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon 2018-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 145 163 25 30 196 3360 23 711 0 0 0 0 341 3523 48 741 False -short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 175 220 51 60 350 6657 85 1602 0 0 0 0 525 6877 136 1662 False -shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill 2017-10-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 Genome assembly Genomics, Microbiology, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46125 47376 2273 2356 40577 40577 3971 3971 19960 21130 1085 1199 106662 109083 7329 7526 False -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 27232 36366 2184 2789 16648 84460 4191 18767 2785 3276 373 452 46665 124102 6748 22008 False -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1620 2660 378 589 10551 24579 682 1851 284 398 67 83 12455 27637 1127 2523 False -sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 276 379 30 42 972 9053 146 1008 644 689 5 7 1892 10121 181 1057 False -sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle 2015-11-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 Sequence trimming Data quality management 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18184 18937 555 608 10514 10514 1063 1063 0 0 0 0 28698 29451 1618 1671 False -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext 2021-02-28 iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 0 2 4 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 220 220 68 68 0 0 0 0 416 416 10 10 636 636 78 78 False -sina sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina 2019-10-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1369 1369 125 125 2398 2398 420 420 0 0 0 0 3767 3767 545 545 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -sistr_cmd sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd 2017-02-20 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3457 3457 301 301 0 0 0 0 556 556 65 65 4013 4013 366 366 False -sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill 2016-10-11 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 312 312 71 71 0 0 0 0 0 0 0 0 312 312 71 71 False -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn 2021-04-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 30 14 31 16 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 82169 116810 2402 2666 18101 18101 2375 2375 17549 17549 321 321 117819 152460 5098 5362 False -skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor 2024-02-07 workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 False -slice_image ip_slice_image Slice image galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image 0.3-4 scikit-image Image analysis Imaging, Bioinformatics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 96 103 4 5 0 0 0 0 4 4 1 1 100 107 5 6 False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters 2019-10-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps 2018-11-25 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures 2017-09-06 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities 2023-05-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 8 8 0 0 0 0 0 0 0 0 158 158 8 8 False -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt 2017-09-19 nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains 2017-05-12 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina 2017-07-07 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 499 499 16 16 44 44 10 10 0 0 0 0 543 543 26 26 False -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes 2019-04-15 climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics To update https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot 2022-06-30 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.3.0 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 325 325 61 61 137 137 54 54 843 843 63 63 1305 1305 178 178 False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap 2017-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 Gene prediction DNA polymorphism, Genetics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1638 331 358 779 779 244 244 467 467 83 83 2745 2884 658 685 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -sniffles sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing Up-to-date https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles 2020-08-29 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 2.4 sniffles 2.4 Sequence analysis, Structural variation detection Sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1141 1141 134 134 606 606 156 156 2267 2267 80 80 4014 4014 370 370 False -snipit snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit 2022-07-17 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 Base position variability plotting Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 905 905 44 44 0 0 0 0 0 0 0 0 905 905 44 44 False -snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy 2019-04-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 121363 124773 3448 3602 92504 92504 3945 3945 48068 52034 2705 3073 261935 269311 10098 10620 False -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists 2019-10-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6555 6555 807 807 5336 5336 171 171 1143 1143 182 182 13034 13034 1160 1160 False -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites 2017-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6597 6597 663 663 1467 1467 256 256 1279 1279 114 114 9343 9343 1033 1033 False -snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff 2018-07-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 5 5 5 5 5 5 5 5 0 0 0 0 0 1 0 0 0 5 5 0 0 5 0 0 0 5 0 0 0 0 0 0 5 5 5 0 103826 108296 7181 7908 115727 178110 15871 22769 11817 13155 2148 2321 231370 299561 25200 32998 False -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 2020-06-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 SNP detection DNA polymorphism, Nucleic acid sites, features and motifs 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 764895 764895 1276 1276 94572 94572 1636 1636 26990 26990 561 561 886457 886457 3473 3473 False -snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 44 10 12 307 649 68 181 227 260 16 23 569 953 94 216 False -snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region To update https://github.com/BrownfieldPlantLab/SNPFreqPlot Variant Analysis snpfreqplot 2020-12-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 3683 3683 338 338 1401 1401 433 433 1029 1029 95 95 6113 6113 866 866 False -snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift 2015-04-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 8 8 8 8 8 8 8 8 0 0 0 0 0 8 0 0 0 0 8 0 0 8 0 0 0 8 0 0 0 0 0 0 8 8 8 0 5142904 5146618 3602 4283 382391 421190 7013 9678 104030 105024 960 1184 5629325 5672832 11575 15145 False -snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 52 55 23 24 421 421 75 75 0 0 0 0 473 476 98 99 False -snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets 2014-11-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 509 554 107 128 474 474 190 190 0 0 0 0 983 1028 297 318 False -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix 2016-01-21 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv 2021-03-07 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 659 659 42 42 296 296 92 92 0 0 0 0 955 955 134 134 False -sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping 2021-09-16 iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics To update http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna 2016-03-17 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.7 Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 19865 21034 1047 1126 3141 3141 328 328 3304 3304 189 189 26310 27479 1564 1643 False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, metaplasmidspades, rnaspades, metaspades, spades, coronaspades, metaviralspades, biosyntheticspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2017-06-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 9 9 9 9 9 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 257254 269129 28813 29969 False -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer 2019-12-18 nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln 2019-01-11 iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 450 491 91 100 4270 4270 288 288 0 0 0 0 4720 4761 379 388 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper 2023-03-16 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec 2022-12-07 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt 2015-04-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv 2015-02-06 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -split_file_on_column tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5995 6261 408 453 2150 2150 311 311 26 26 2 2 8171 8437 721 766 False -split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection 2019-08-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 16415 16623 968 984 9133 9133 672 672 4140 4140 148 148 29688 29896 1788 1804 False -split_labelmap ip_split_labelmap Split Labelmaps galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap 2018-12-11 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap 0.2-3 scikit-image Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 44 51 2 3 0 0 0 0 0 0 0 0 44 51 2 3 False -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 3 200 384 31 66 200 397 31 69 False -splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta 2015-10-16 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1772 1811 278 294 3012 3012 564 564 0 0 0 0 4784 4823 842 858 False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ 2019-05-23 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 789 840 130 134 0 0 0 0 0 0 0 0 789 840 130 134 False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred 2015-12-14 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d 2021-07-20 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d 0.1 giatools 0.3.1 Image analysis Imaging, Bioinformatics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 16 4 4 0 0 0 0 0 0 0 0 16 16 4 4 False -spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping 2018-05-07 iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1436 1436 23 23 0 0 0 0 0 0 0 0 1436 1436 23 23 False -spyboat spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat 2020-11-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 142 142 5 5 0 0 0 0 0 0 0 0 142 142 5 5 False -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie 2017-09-02 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 80 1 1 0 0 0 0 80 80 1 1 False -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation 2017-09-11 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools 2020-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 Data handling DNA, Genomics, Sequencing 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 2 0 3 0 0 3 0 0 0 3 0 0 0 0 0 0 3 3 3 0 364871 376580 16710 17342 583675 678448 53271 59638 48131 50455 5910 6181 996677 1105483 75891 83161 False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology 2022-12-30 ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base 4 0 7 7 4 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 239 239 34 34 44 44 13 13 0 0 0 0 283 283 47 47 False -srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 2015-12-02 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 2022-08-22 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.21 Multilocus sequence typing Whole genome sequencing, Public health and epidemiology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 297 297 40 40 71 71 1 1 0 0 0 0 368 368 41 41 False -sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm 2018-07-05 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 214 225 17 18 0 0 0 0 0 0 0 0 214 225 17 18 False -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks 2017-04-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 Data handling Mapping, Population genetics 0 13 13 12 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 6440 11998 465 593 0 0 0 0 4070 4070 76 76 10510 16068 541 669 False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis 2019-09-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 0 12 12 12 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 8437 8592 626 646 0 0 0 0 18016 18016 270 270 26453 26608 896 916 False -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 False -staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr 2022-06-10 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20778 20891 2030 2045 9520 9520 1424 1424 6753 6753 864 864 37051 37164 4318 4333 False -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing 2015-02-28 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 169 346 46 61 0 0 0 0 0 0 0 0 169 346 46 61 False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps 2020-03-27 ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 0 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 328 328 38 38 0 0 0 0 0 0 0 0 328 328 38 38 False -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign 2022-10-02 iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka 2021-01-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 669 669 112 112 1261 1261 417 417 0 0 0 0 1930 1930 529 529 False -stress_ng stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng 2021-03-04 bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 3 3 0 0 0 0 0 0 0 0 62 62 3 3 False -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst 2016-10-19 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 False -structure structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date https://web.stanford.edu/group/pritchardlab/structure.html Phylogenetics, Variant Analysis structure 2017-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 Genetic variation analysis Population genetics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2858 3001 118 123 0 0 0 0 0 0 0 0 2858 3001 118 123 False -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ Phylogenetics, Variant Analysis structureharvester 2017-12-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 3901 34 747 105 114 4 4 226 4015 38 751 False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 901 13 84 0 0 0 0 93 901 13 84 False -subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 566512 567199 410 470 49985 184650 1473 7631 20648 20897 155 188 637145 772746 2038 8289 False -subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.13.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1178 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https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 4 4 4 2 4 4 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 117 117 41 41 84 84 24 24 161 161 13 13 362 362 78 78 False -suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 217 217 47 47 42 42 20 20 96 96 12 12 355 355 79 79 False -suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 721 721 160 160 350 350 91 91 214 214 35 35 1285 1285 286 286 False -suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 125 125 30 30 13 13 9 9 83 83 8 8 221 221 47 47 False -suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 396 396 134 134 121 121 57 57 144 144 39 39 661 661 230 230 False -suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 21 21 22 21 21 21 22 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 964 964 318 318 249 249 118 118 475 475 108 108 1688 1688 544 544 False -suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 8 8 8 8 13 13 11 11 1302 1302 19 19 1323 1323 38 38 False -suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 58 58 23 23 24 24 11 11 92 92 11 11 174 174 45 45 False -suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 10 10 10 10 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 863 863 220 220 237 237 98 98 181 181 41 41 1281 1281 359 359 False -suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 17 17 17 17 17 17 17 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 983 983 287 287 375 375 144 144 907 907 106 106 2265 2265 537 537 False -suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 46 46 13 13 9 9 5 5 0 0 0 0 55 55 18 18 False -suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 11 11 11 11 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 37 37 16 16 22 22 7 7 89 89 14 14 148 148 37 37 False -suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 615 615 143 143 246 246 75 75 115 115 27 27 976 976 245 245 False -suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 12 12 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 330 330 83 83 64 64 40 40 195 195 49 49 589 589 172 172 False -suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 6 6 6 6 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 4 4 5 5 5 5 1 1 1 1 10 10 10 10 False -suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 14 14 16 16 6 6 37 37 2 2 82 82 22 22 False -suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics 2024-04-25 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 10 10 3 3 14 14 10 10 5 5 5 5 29 29 18 18 False -suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 4 4 4 4 4 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 664 664 145 145 113 113 43 43 255 255 50 50 1032 1032 238 238 False -suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.5.0+q2galaxy.2024.5.0 8 8 8 7 8 8 8 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 84 84 52 52 25 25 16 16 9 9 5 5 118 118 73 73 False -suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis 2022-08-29 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics 2022-08-26 q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.5.0+dist.he540b0b0 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 14941 14941 383 383 25941 25941 255 255 2856 2856 112 112 43738 43738 750 750 False -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 2015-09-10 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm 2023-07-05 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm 0.2.0 superdsm 0.4.0 Image analysis 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 5 5 0 0 0 0 0 0 0 0 26 26 5 5 False -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink 2017-11-21 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva 2022-06-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 2 2 0 0 0 0 0 0 0 0 30 30 2 2 False -t2ps Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 Phylogenetic tree visualisation Phylogenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 411 472 68 90 102 7952 13 1240 0 0 0 0 513 8424 81 1330 False -t2t_report t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 927 959 65 78 130 7194 18 1143 0 0 0 0 1057 8153 83 1221 False -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee 2016-12-13 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3783 9125 211 229 1 1 1 1 0 0 0 0 3784 9126 212 230 False -t_test_two_samples t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 141 215 20 31 520 1166 79 274 1025 1118 11 12 1686 2499 110 317 False -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar 2013-12-02 devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16526 64515 2803 7456 0 0 0 0 16526 64515 2803 7456 False -table_compute table_compute Perform general-purpose table operations To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute Text Manipulation table_compute 2019-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 216072 216115 1811 1814 12326 12326 1558 1558 16136 16136 256 256 244534 244577 3625 3628 False -tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2188 2220 33 38 0 0 0 0 0 0 0 0 2188 2220 33 38 False -tabular_to_fasta tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta 2014-05-19 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 329032 333057 1489 1702 79033 215770 2441 8587 27876 33727 296 360 435941 582554 4226 10649 False -tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter To update https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq 2019-06-21 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.2.0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7011 8135 449 482 9473 28494 626 2183 850 1090 80 104 17334 37719 1155 2769 False -tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency 2016-05-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 158 164 15 16 722 865 40 73 0 0 0 0 880 1029 55 89 False -tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan 2024-02-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 6 6 0 0 0 0 0 0 0 0 19 19 6 6 False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 2021-05-05 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -targetfinder targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder 2015-10-23 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 827 838 89 92 114 114 41 41 900 900 29 29 1841 1852 159 162 False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date https://github.com/nebiolabs/tasmanian-mismatch Sequence Analysis tasmanian_mismatch 2020-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 61 61 7 7 0 0 0 0 65 65 11 11 False -taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Up-to-date https://bioinf.shenwei.me/taxonkit/ Metagenomics taxonkit 2024-07-26 iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit 0.17.0 taxonkit 0.17.0 Formatting, Data retrieval Taxonomy, Biotechnology, Ecology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq 2019-01-13 iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart 2015-08-12 crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 Visualisation Metagenomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 1 0 36069 36922 5257 5431 25255 30822 5066 5826 7949 7949 1584 1584 69273 75693 11907 12841 False -taxpasta taxpasta standardise taxonomic profiles taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Up-to-date https://taxpasta.readthedocs.io/en/latest/ Sequence Analysis taxpasta 2023-08-30 iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta 0.7.0 taxpasta 0.7.0 Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 5 5 0 0 0 0 0 0 0 0 34 34 5 5 False -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler 2019-08-16 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.3.0 Antimicrobial resistance prediction 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6372 6395 372 379 7339 7339 378 378 6966 6966 154 154 20677 20700 904 911 False -tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter 2019-10-03 iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22977 22977 461 461 3888 3888 274 274 3611 3611 80 80 30476 30476 815 815 False -tbl2gff3 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 2020-07-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1941 1941 466 466 0 0 0 0 463 463 112 112 2404 2404 578 578 False -tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport 2019-08-29 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.1 tbvcfreport 1.0.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2955 2955 335 335 6090 6090 348 348 2347 2347 72 72 11392 11392 755 755 False -te_finder te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder 2022-08-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.21 Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 20 20 0 0 0 0 0 0 0 0 203 203 20 20 False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign 2019-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit 2020-04-10 iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1013 1013 74 74 0 0 0 0 70 70 4 4 1083 1083 78 78 False -tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper 2019-11-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 106 16 16 155 155 47 47 0 0 0 0 261 261 63 63 False -text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing 2019-01-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 20 20 20 20 20 20 20 20 0 0 0 0 0 0 0 0 19 1 19 0 0 19 0 0 0 20 0 0 0 0 0 0 19 19 19 0 3898014 4015573 37698 42095 648268 915282 47636 69828 103365 105214 7778 7953 4649647 5036069 93112 119876 False -tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser 2021-11-14 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 547 547 51 51 0 0 0 0 0 0 0 0 547 547 51 51 False -tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara 2024-05-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 8 8 0 0 0 0 0 0 0 0 15 15 8 8 False -tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences Up-to-date https://github.com/veg/tn93/ Sequence Analysis tn93 2018-06-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.14 tn93 1.0.14 4 0 4 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 4 0 0 1915 1915 42 42 1972 1972 225 225 0 0 0 0 3887 3887 267 267 False -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model 2019-08-23 bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 445 445 25 25 71 71 32 32 0 0 0 0 516 516 57 57 False -tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator 2024-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.9.1 tooldistillator 0.9.1 Parsing Microbiology, Bioinformatics, Sequence analysis 2 0 2 2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 9 9 6 6 5 5 0 0 0 0 71 71 14 14 False -tophat tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 158 66524 28 7228 0 0 0 0 158 66525 28 7229 False -tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 2014-10-15 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 15496 26623 1076 1664 83063 343017 8372 27829 5388 14057 508 1012 103947 383697 9956 30505 False -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 False -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors 2021-12-23 chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 57 57 10 10 20 20 8 8 0 0 0 0 77 77 18 18 False -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics 2024-03-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.4 tracegroomer 0.1.4 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 1 1 0 0 0 0 0 0 0 0 7 7 1 1 False -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update 2021-10-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.8 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 3314 3314 124 124 0 0 0 0 0 0 0 0 3314 3314 124 124 False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation 2019-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 Transposon prediction DNA, Sequencing, Mobile genetic elements 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 1039 1039 189 189 2672 3349 467 485 358 358 47 47 4069 4746 703 721 False -translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed 2018-01-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 649 685 138 142 473 473 105 105 761 761 18 18 1883 1919 261 265 False -translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences 2016-01-13 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 69 16 21 0 0 0 0 0 0 0 0 57 69 16 21 False -transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp 2015-10-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 Transcriptional regulatory element prediction Transcription factors and regulatory sites 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 250 254 31 31 174 174 45 45 0 0 0 0 424 428 76 76 False -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler 2019-04-15 nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore 2015-04-22 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 Sequence trimming, Primer removal, Read pre-processing Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 229489 275008 5733 6500 228708 324716 11708 16638 22644 23869 1439 1527 480841 623593 18880 24665 False -trimmer trimmer Trim leading or trailing characters. To update Text Manipulation trimmer 2012-12-04 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 1 1 1 1 5304 7438 447 512 15698 108672 658 2946 266 822 53 81 21268 116932 1158 3539 False -trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic 2024-01-03 pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 352353 383014 14547 15408 632385 839058 39323 49850 125340 139097 5268 5975 1110078 1361169 59138 71233 False -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 False -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services 2018-06-20 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction 2015-05-08 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 0 2 2 0 0 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 4361 4601 741 807 0 0 0 0 2469 2469 190 190 6830 7070 931 997 False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler 2021-02-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 0 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 14681 14681 265 265 0 0 0 0 4488 4488 147 147 19169 19169 412 412 False -tsebra tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation 2023-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.5 tsebra 1.1.2.5 Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 7 7 0 0 0 0 0 0 0 0 17 17 7 7 False -tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne 2017-05-26 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 255 379 31 37 281 281 64 64 0 0 0 0 536 660 95 101 False -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa 2016-08-19 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 469 ucsc-twobittofa 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 413 511 84 118 441 441 123 123 21 21 2 2 875 973 209 243 False -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 False -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 False -ucsc_axtchain ucsc_axtchain Chain together genome alignments UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_axtchain 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain 469 ucsc-axtchain 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_axttomaf 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf 469 ucsc-axttomaf 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis Up-to-date http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat 2017-05-17 yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 469 ucsc-blat 469 Sequence alignment Sequence analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainnet ucsc_chainnet Make alignment nets out of chains UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainnet 2024-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet 469 ucsc-chainnet 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainprenet 2024-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet 469 ucsc-chainprenet 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_chainsort 2024-08-26 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort 469 ucsc-chainsort 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 373 463 134 151 2249 18611 638 4080 0 0 0 0 2622 19074 772 4231 False -ucsc_netfilter ucsc_netfilter Filter out parts of net UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netfilter 2024-09-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter 469 ucsc-netfilter 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Sequence Analysis ucsc_netsyntenic 2024-09-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic 469 ucsc-netsyntenic 469 Sequence analysis 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_nettoaxt 2024-09-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt 469 ucsc-nettoaxt 469 Sequence analysis 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler 2018-08-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.1 unicycler 0.5.1 Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 74120 77648 3798 3963 64946 90075 5451 7380 19516 20422 2010 2080 158582 188145 11259 13423 False -unipept unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept 2015-04-03 galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4900 5146 257 270 251 251 81 81 1069 1069 29 29 6220 6466 367 380 False -uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface 2015-10-09 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.6 requests 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2117 2725 341 412 3111 5779 594 1011 806 806 50 50 6034 9310 985 1473 False -uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader 2016-03-08 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1488 1596 230 266 0 0 0 0 743 743 35 35 2231 2339 265 301 False -unzip unzip Unzip file To update https://github.com/bmcv Convert Formats unzip 2019-08-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 6.0 unzip 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6942 7024 1345 1356 1 1 1 1 2461 2461 266 266 9404 9486 1612 1623 False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero 2022-01-18 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -usher usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher 2021-05-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Cladistics, Genotype and phenotype, Phylogenomics 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1060 1060 5 5 0 0 0 0 0 0 0 0 1060 1060 5 5 False -valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet 2017-11-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 518 677 75 87 234 234 65 65 0 0 0 0 752 911 140 152 False -validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database 2017-09-14 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 112 112 38 38 0 0 0 0 0 0 0 0 112 112 38 38 False -vapor vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor 2022-08-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5936 5936 147 147 523 523 15 15 0 0 0 0 6459 6459 162 162 False -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java 2020-08-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 381 381 37 37 0 0 0 0 0 0 0 0 381 381 37 37 False -variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer 2019-11-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 95 95 14 14 516 516 67 67 0 0 0 0 611 611 81 81 False -varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan 2018-11-29 iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 10711 11502 1442 1560 16705 16705 3135 3135 1036 1036 100 100 28452 29243 4677 4795 False -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf 2022-11-28 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 2013-11-17 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5058 6139 606 699 17232 53268 2965 5686 2298 2656 424 482 24588 62063 3995 6867 False -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology, Probes and primers To update https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp 2024-01-27 iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.1 PCR primer design Virology, Probes and primers 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 273 273 12 12 0 0 0 0 0 0 0 0 273 273 12 12 False -vcf2maf vcf2maf vcf2maf: Convert VCF into MAF To update https://github.com/mskcc/vcf2maf Convert Formats vcf2maf 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1097 1097 46 46 0 0 0 0 65 65 5 5 1162 1162 51 51 False -vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp 2014-07-28 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 191 221 57 65 1399 2700 209 584 0 0 0 0 1590 2921 266 649 False -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment 2016-01-20 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 169090 169679 823 874 16304 42215 1141 2594 2485 2511 169 172 187879 214405 2133 3640 False -vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 263 340 31 54 263 342 31 56 False -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 513 569 6 9 513 569 6 9 False -vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 400 455 129 140 0 0 0 0 238 606 19 56 638 1061 148 196 False -vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 3 0 0 0 0 335 463 19 28 335 482 19 31 False -vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 882 888 30 32 6118 8261 36 114 175 184 6 6 7175 9333 72 152 False -vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 6879 17157 897 1219 7585 14509 1245 1925 1648 1681 225 229 16112 33347 2367 3373 False -vcfanno vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno 2021-01-17 iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 SNP annotation Genetic variation, Data submission, annotation and curation 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1139 1139 174 174 0 0 0 0 0 0 0 0 1139 1139 174 174 False -vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2797 2850 157 181 3668 14532 652 1392 494 507 61 63 6959 17889 870 1636 False -vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 189 203 62 66 497 1828 155 387 184 197 11 11 870 2228 228 464 False -vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3017 4049 185 210 4709 20250 406 1147 507 527 40 42 8233 24826 631 1399 False -vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 416 478 35 40 3969 10457 82 309 362 378 8 8 4747 11313 125 357 False -vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 745 767 96 106 803 1895 222 627 241 256 16 17 1789 2918 334 750 False -vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1422 2020 284 505 4951 19530 1021 2669 493 516 60 62 6866 22066 1365 3236 False -vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 233 253 37 42 234 1839 79 287 199 214 11 12 666 2306 127 341 False -vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 572 585 90 92 2063 2427 139 296 272 290 19 22 2907 3302 248 410 False -vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37489 47142 2113 2218 75128 162296 5730 10533 2626 2736 320 331 115243 212174 8163 13082 False -vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 926 957 155 173 2291 5323 313 985 251 265 28 31 3468 6545 496 1189 False -vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 172 183 21 25 351 879 67 201 312 342 15 16 835 1404 103 242 False -vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 778 794 107 112 2414 3721 179 508 209 225 20 21 3401 4740 306 641 False -vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 502 555 134 143 3428 6338 266 858 220 235 23 24 4150 7128 423 1025 False -vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1964 1991 182 186 1937 3846 188 644 567 601 26 27 4468 6438 396 857 False -vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 269 310 38 42 358 1071 89 287 179 213 12 14 806 1594 139 343 False -vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 590 711 28 33 403 831 75 200 190 214 10 12 1183 1756 113 245 False -vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 161 168 13 15 153 350 27 75 184 192 6 6 498 710 46 96 False -vcfselectsamples vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 830 900 69 88 1315 6257 237 959 344 363 20 21 2489 7520 326 1068 False -vcfsort vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1868 1904 174 185 18378 24175 422 1279 537 674 70 73 20783 26753 666 1537 False -vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 192 81 90 1853 3943 581 1280 144 156 13 16 2152 4291 675 1386 False -vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 440 594 127 142 0 0 0 0 0 16 0 12 440 610 127 154 False -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus 2016-10-16 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vcftools_isec vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 379 537 104 118 0 1 0 1 39 496 28 48 418 1034 132 167 False -vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 817 1084 244 273 0 0 0 0 93 448 44 60 910 1532 288 333 False -vcftools_slice vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 410 423 56 60 6261 8115 133 362 127 157 10 19 6798 8695 199 441 False -vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset 2013-11-24 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 142 46 49 0 0 0 0 120 142 12 19 254 284 58 68 False -vcfvcfintersect vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect 2017-01-24 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.10 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 976544 977015 703 748 64155 81830 981 2103 11044 11069 225 229 1051743 1069914 1909 3080 False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics 2015-08-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science 3 0 3 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 2157 2287 198 209 3930 5591 446 744 0 0 0 0 6087 7878 644 953 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False -velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet 2020-06-09 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 Formatting, De-novo assembly Sequence assembly 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 25171 27943 3899 4270 51187 51187 7557 7557 28546 28619 3585 3613 104904 107749 15041 15440 False -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser 2017-12-19 simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 Optimisation and refinement, Sequence assembly Genomics, Sequence assembly 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4715 5343 888 965 9575 9576 2117 2117 3271 5524 1050 1397 17561 20443 4055 4479 False -venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list 2015-12-08 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 1 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 4519 5476 667 730 9858 18420 986 2010 0 0 0 0 14377 23896 1653 2740 False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map 2015-10-28 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -verkko verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko 2023-01-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.2.1 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 25 25 0 0 0 0 0 0 0 0 48 48 25 25 False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis 2020-04-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.59.0 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 478 478 17 17 0 0 0 0 0 0 0 0 478 478 17 17 False -vibrant vibrant Virus Identification By iteRative ANnoTation VIBRANT VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Up-to-date https://github.com/AnantharamanLab/VIBRANT Metagenomics vibrant 2024-09-11 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant 1.2.1 vibrant 1.2.1 Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna 2017-08-19 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 0 0 21 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 3197 8107 344 415 0 0 0 0 0 0 0 0 3197 8107 344 415 False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro 2019-03-13 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 0 0 4 4 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 14412 14590 722 732 0 0 0 0 0 0 0 0 14412 14590 722 732 False -virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot 2024-03-04 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.1.0+galaxy0 biopython 1.70 Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology 0 0 3 3 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 94 16 16 0 0 0 0 0 0 0 0 94 94 16 16 False -virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat 2024-05-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7.1 virheat 0.7.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 2 2 0 0 0 0 0 0 0 0 12 12 2 2 False -virhunter virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter 2022-09-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy Sequence classification Virology 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 574 574 76 76 0 0 0 0 0 0 0 0 574 574 76 76 False -virsorter virsorter VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. virsorter virsorter virsorter Identify DNA and RNA virus sequences. Taxonomic classification Metagenomics Up-to-date https://github.com/jiarong/VirSorter2/ Metagenomics virsorter 2024-06-20 ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter 2.2.4 virsorter 2.2.4 Taxonomic classification Metagenomics 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool evaluatesegmentation-tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation 2024-09-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 20 25 1 1 0 0 0 0 0 0 0 0 20 25 1 1 False -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd 2019-10-24 chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 False -voronoi_tessellation voronoi_tessellation Compute Voronoi tesselation scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging voronoi_tesselation 2024-03-09 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation 0.22.0 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 43 3 3 0 0 0 0 0 0 0 0 43 43 3 3 False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch 2015-07-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.29.0 DNA mapping, Chimera detection Metagenomics, Sequence analysis 8 8 8 8 8 8 8 8 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 9694 10338 559 628 12282 53546 1031 2007 5334 5672 246 277 27310 69556 1836 2912 False -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp 2020-04-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt 2015-02-28 bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mclassfilter w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter 2019-09-26 eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2370 2836 9 10 0 0 0 0 1482 1509 4 4 3852 4345 13 14 False -w4mconcatenate W4Mconcatenate [W4M][Utils] concatenate two Metadata tables To update http://workflow4metabolomics.org Metabolomics w4mconcatenate 2024-07-10 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate 1.0.0+galaxy0 r-base 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -w4mcorcov w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov 2018-09-05 eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 238 375 10 10 0 0 0 0 10 10 2 2 248 385 12 12 False -w4mjoinpn w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn 2018-08-06 eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 150 171 7 7 0 0 0 0 7 7 2 2 157 178 9 9 False -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade 2019-09-20 nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics 2022-09-19 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 Standardisation and normalisation Metabolomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 39 39 6 6 4 4 3 3 0 0 0 0 43 43 9 9 False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather 2016-07-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -weblogo3 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 2017-11-17 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2720 2818 206 228 10299 30578 1354 3657 1226 1285 50 59 14245 34681 1610 3944 False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 2307 17 75 0 0 0 0 227 2307 17 75 False -whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper 2024-04-23 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 13 13 0 0 0 0 0 0 0 0 96 96 13 13 False -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig 2024-01-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 469 ucsc-wigtobigwig 469 Sequence analysis 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1601 1601 106 106 1108 1108 172 172 200 200 15 15 2909 2909 293 293 False -windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker 2023-12-14 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.16.0 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 537 537 19 19 12 12 7 7 297 297 2 2 846 846 28 28 False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter 2014-04-01 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.13.0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 171 3961 34 328 0 0 0 0 171 3972 34 330 False -winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap 2021-04-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 279 279 46 46 12 12 4 4 0 0 0 0 291 291 50 50 False -woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis 2024-02-29 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 1 1 0 0 0 0 0 0 0 0 31 31 1 1 False -wsi_extract_top_view ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view 2017-10-30 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view 0.2-2 scikit-image 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 38 2 3 0 0 0 0 0 0 0 0 32 38 2 3 False -wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg 2018-06-12 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 Genome assembly, De-novo assembly Sequence assembly, Sequencing 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1619 1715 337 376 0 0 0 0 0 0 0 0 1619 1715 337 376 False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology 2022-07-06 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray 5 2 6 5 5 2 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 2 0 5995 5995 275 275 66 66 23 23 295 295 3 3 6356 6356 301 301 False -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw XCMS XCMS xcms Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Biological imaging, Data visualisation, Metabolomics Up-to-date https://github.com/sneumann/xcms Metabolomics xcms 2023-05-24 workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 4.0.0 bioconductor-xcms 4.0.0 Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation Data visualisation, Metabolomics 9 11 12 12 9 11 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 10 9 0 31909 35790 1357 1384 7099 7099 413 413 5333 5357 330 330 44341 48246 2100 2127 False -xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet 2021-10-18 ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 17 17 0 0 0 0 0 0 0 0 59 59 17 17 False -xpath xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath 2015-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 235 7 8 0 1 0 1 0 0 0 0 128 236 7 9 False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore 2021-05-26 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization 2023-09-06 recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb 0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 143 143 4 4 0 0 0 0 0 0 0 0 143 143 4 4 False -xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot 2013-09-25 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4490 6169 768 889 6120 15516 1921 3653 2033 2212 556 590 12643 23897 3245 5132 False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper 2015-06-17 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -yahs yahs Yet Another Hi-C scaffolding tool To update https://github.com/c-zhou/yahs Assembly yahs 2022-06-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2.2 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 618 618 176 176 336 336 62 62 588 588 25 25 1542 1542 263 263 False -zeiss_lmd_converter ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter Proteomics 2024-06-29 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 1 1 0 0 0 0 0 0 0 0 4 4 1 1 False -zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone 2018-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 83 96 9 12 0 0 0 0 0 0 0 0 83 96 9 12 False -zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology 2024-05-03 ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 4 4 0 0 0 0 0 0 0 0 26 26 4 4 False +Galaxy wrapper id Description To keep Deprecated +ThermoRawFileParser Thermo RAW file converter +b2btools This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. +bed_to_protein_map Converts a BED file to a tabular list of exon locations +bumbershoot +calisp Calgary approach to isotopes in proteomics +cardinal Statistical and computational tools for analyzing mass spectrometry imaging datasets +cite_seq_count Count CMO/HTO +colabfold Protein prediction based on AlphaFold2 +custom_pro_db CustomProDB +custom_pro_db_annotation_data_manager CustomProDB Annotation +data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper +data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper +dbbuilder Protein Database Downloader +decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. +dia_umpire DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics +dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. +diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. +diapysef diapysef is a convenience package for working with DIA-PASEF data +diffacto Diffacto comparative protein abundance estimation +dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence +eggnog_mapper eggnog-mapper fast functional annotation of novel sequences +encyclopedia Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis +fastg2protlib Generate FASTA from FASTG +feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy +filter_by_fasta_ids Filter FASTA on the headers and/or the sequences +flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification +fragpipe Data analysis for mass spectrometry-based proteomics. +hardklor Hardklör +idconvert Convert mass spectrometry identification files on linux or MacOSX +improviser Visualisation of PepXML files +lfq_protein_quant Enable protein summarisation and quantitation +maldiquant MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. +map_peptides_to_bed Map peptides to a reference genome for display by a genome browser +maxquant wrapper for MaxQuant +meta_proteome_analyzer MetaProteomeAnalyzer +metanovo Produce targeted databases for mass spectrometry analysis. +metaquantome quantitative analysis of microbiome taxonomy and function +moFF moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. +morpheus Morpheus MS Search Application +mqppep MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA +msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container +msgfplus MSGF+ +msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. +msstats MSstats tool for analyzing mass spectrometry proteomic datasets +msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling +mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome +multigsea GSEA-based pathway enrichment analysis for multi-omics data +mz_to_sqlite Creates a SQLite database for proteomics data +mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. +openms OpenMS in version 2.1. +openms OpenMS Suite for LC/MS data management and analyses +pathwaymatcher Reactome Pathway Matcher +pep_pointer PepPointer categorizes peptides by their genomic coordinates. +pepquery A peptide-centric MS search engine for novel peptide identification and validation. +pepquery2 PepQuery2 peptide-centric MS search for peptide identification and validation +peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files +peptideshaker PeptideShaker and SearchGUI +peptimapper Proteogenomics workflow for the expert annotation of eukaryotic genomes +pepxml_to_xls Convert PepXML to Tabular +percolator Percolator +pi_db_tools HiRIEF tools +pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS +prot-scriber Protein annotation of short human readable descriptions +protease_prediction This tool can learn the cleavage specificity of a given class of proteases. +proteinortho Proteinortho is a tool to detect orthologous proteins/genes within different species. +proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. +proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. +proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. +proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. +proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. +proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. +proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. +proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. +proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. +proteore_venn_diagram ProteoRE JVenn Diagram +psm2sam PSM to SAM +psm_validation Validate PSM from Ion Fragmentation +pyprophet Semi-supervised learning and scoring of OpenSWATH results. +pyteomics Tools using the pyteomics library +quantp Correlation between protein and transcript abundance +quantwiz_iq Isobaric Quantitation using QuantWiz-IQ +rawtools Raw Tools +sixgill Six-frame Genome-Inferred Libraries for LC-MS/MS +spectrast2spectrast_irt Filter from spectraST files to swath input files +spectrast2tsv Filter from spectraST files to swath input files +syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. +tapscan Search for transcription associated proteins (TAPs) +translate_bed Translate BED transcript CDS or cDNA in 3 frames +translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column +unipept Unipept retrieves metaproteomics information +uniprot_rest_interface UniProt ID mapping and sequence retrieval +uniprotxml_downloader Download UniProt proteome in XML or fasta format +validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. +zeiss_lmd_converter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems diff --git a/communities/spoc/metadata/tool_status.tsv b/communities/spoc/metadata/tool_status.tsv index 7faf75ee..ccfde0e6 100644 --- a/communities/spoc/metadata/tool_status.tsv +++ b/communities/spoc/metadata/tool_status.tsv @@ -1,3 +1,4 @@ + To keep Deprecated aegean FALSE FALSE anndata TRUE FALSE arriba FALSE FALSE diff --git a/communities/spoc/resources/tools.tsv b/communities/spoc/resources/curated_tools.tsv similarity index 94% rename from communities/spoc/resources/tools.tsv rename to communities/spoc/resources/curated_tools.tsv index c0645bef..4c518d4e 100644 --- a/communities/spoc/resources/tools.tsv +++ b/communities/spoc/resources/curated_tools.tsv @@ -1,59 +1,59 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True +Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed To keep Deprecated +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True True False +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True True False +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True True False +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True True False +cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True True False +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True True False +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True True False +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True True False +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True True False +deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True True False +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True True False +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True True False +dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True True False +dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True True False +edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True True False +egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True True False +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True True False +fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True True False +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True True False +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True True False +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True True False +infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True True False +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True True False +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True True False +music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True True False +pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True True False +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True True False +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True True False +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True True False +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True True False +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True True False +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True True False +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True True False +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True True False +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True True False +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True True False +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True True False +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True True False +scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True True False +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True True False +seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True True False +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True True False +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True True False +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True True False +spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True True False +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True True False +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True True False +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True True False +volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True True False diff --git a/communities/spoc/resources/curated_tools_w_biotools.tsv b/communities/spoc/resources/curated_tools_w_biotools.tsv new file mode 100644 index 00000000..1fbeb11c --- /dev/null +++ b/communities/spoc/resources/curated_tools_w_biotools.tsv @@ -0,0 +1,19 @@ +Galaxy wrapper id bio.tool name EDAM operation EDAM topic +baredsc baredSC Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability +cemitool CEMiTool Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment +cite_seq_count CITE-seq-Count RNA-Seq quantification Transcriptomics, Immunoproteins and antigens +deseq2 DESeq2 Differential gene expression analysis, RNA-Seq analysis RNA-Seq +dexseq DEXSeq Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq +dropletutils DropletUtils Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics +edger edgeR Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq +egsea EGSEA Gene set testing Systems biology +episcanpy epiScanpy Enrichment analysis, Imputation Epigenomics, Cell biology, DNA +fgsea fgsea Gene-set enrichment analysis Genetics +heinz Heinz Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks +multigsea multiGSEA Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules +rgrnastar STAR Sequence alignment RNA-Seq, Transcriptomics +salmon Salmon Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics +scanpy SCANPY Differential gene expression analysis Gene expression, Cell biology, Genetics +scater scater Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics +scpipe scPipe Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing +umi_tools UMI-tools Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs diff --git a/communities/spoc/resources/curated_tools_wo_biotools.tsv b/communities/spoc/resources/curated_tools_wo_biotools.tsv new file mode 100644 index 00000000..49d3ff43 --- /dev/null +++ b/communities/spoc/resources/curated_tools_wo_biotools.tsv @@ -0,0 +1,41 @@ +Galaxy wrapper id Source Galaxy wrapper source +anndata https://anndata.readthedocs.io https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ +cell-types-analysis https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +cosg https://github.com/genecell/COSG https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ +crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter +data-hca https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +data-scxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +decoupler https://decoupler-py.readthedocs.io/en/latest/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +deg_annotate https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate +deseq2_normalization http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization +dropletutils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +garnett https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +gsc_filter_cells http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells +gsc_filter_genes http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes +gsc_gene_expression_correlations http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations +gsc_high_dimensions_visualisation http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization +gsc_mannwhitney_de http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de +gsc_scran_normalize http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize +gsc_signature_score http://artbio.fr https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score +infercnv https://github.com/broadinstitute/infercnv https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv +monocle3 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +music_deconvolution https://github.com/xuranw/MuSiC https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ +pyscenic https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +raceid 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all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 True False False -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True -arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 True False False -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 True False False -brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 True False False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True -cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 True False False -chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 True False False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 True False False -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True -cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 True False False -cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 True False False -cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 True False False -cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 True False False -cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 True False False -cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 True False False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True -deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True -deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True -dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True -edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True -egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True False False -fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True -genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 True False False -gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 True False False -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True -infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True -isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 True False False -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 True False False -limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True False False -masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 True False False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 True False False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True -multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True -music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 True False False -pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 True False False -psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 True False False -pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True False False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 True False False -repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 True False False -rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 True False False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True False False -ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 True False False -salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True -seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True -slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 True False False -sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 True False False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True -star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 True False False -stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 True False False -tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 True False False -transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 True False False -trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 True False False -trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 True False False -tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 True False False -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True -volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True +Galaxy wrapper id Description To keep Deprecated +aegean AEGeAn toolkit wrappers False False +anndata Import, Export, Inspect and Manipulate Anndata and Loom objects True False +arriba Arriba detects fusion genes in RNA-Seq data after running RNA-STAR False False +askor AskoR links EdgeR and AskOmics False False +bamparse Generates hit count lists from bam alignments. False False +baredsc baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. True False +bctools bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 False False +brew3r_r Extend 3' end of a GTF using another GTF as a template False False +cell-types-analysis Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis True False +cemitool Gene co-expression network analysis tool True False +cherri Computational Help Evaluating RNA-RNA interactions False False +chira Chimeric Read Annotator for RNA-RNA interactome data False False +cite_seq_count Count CMO/HTO True False +cosg Marker gene identification for single-cell sequencing data using COSG. True False +cpat Coding-potential assessment tool using an alignment-free logistic regression model. False False +cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts False False +crosscontamination_barcode_filter Barcode contamination discovery tool True False +cuffcompare Galaxy wrappers for the Cuffcompare tool. False False +cuffdiff Galaxy wrappers for the Cuffdiff tool. False False +cufflinks Galaxy wrappers for the Cufflinks tool. False False +cuffmerge Galaxy wrappers for the Cuffmerge tool. False False +cuffnorm The Cuffnorm tool False False +cuffquant The Cuffquant tool False False +data-hca Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects True False +data-scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home True False +decoupler decoupler - Ensemble of methods to infer biological activities True False +deg_annotate Annotate DESeq2/DEXSeq output tables True False +deseq2 Differential gene expression analysis based on the negative binomial distribution True False +deseq2_normalization Normalizes gene hitlists True False +dexseq Inference of differential exon usage in RNA-Seq True False +dropletutils De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 True False +dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data True False +edger Perform RNA-Seq differential expression analysis using edgeR pipeline True False +egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing True False +episcanpy EpiScanpy – Epigenomics single cell analysis in python True False +fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. False False +fastq_utils Set of tools for handling fastq files False False +featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome False False +fgsea Perform gene set testing using fgsea True False +garnett De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 True False +genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases False False +gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. False False +gsc_filter_cells Filter single cell RNAseq data on libray depth and number of detected genes True False +gsc_filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data True False +gsc_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations True False +gsc_high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation True False +gsc_mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data True False +gsc_scran_normalize Normalize raw counts using scran True False +gsc_signature_score Compute signature scores from single cell RNAseq data True False +heinz An algorithm for identification of the optimal scoring subnetwork. True False +infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data True False +isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. False False +kallisto kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. False False +limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline False False +masigpro Identify significantly differential expression profiles in time-course microarray experiments False False +mircounts Generates miRNA count lists from read alignments to mirBase. False False +monocle3 De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. True False +multigsea GSEA-based pathway enrichment analysis for multi-omics data True False +music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) True False +nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. False False +pathifier pathifier False False +pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. False False +psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. False False +pyscenic PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ True False +qualimap Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. False False +raceid RaceID3, StemID2, FateID - scRNA analysis True False +repenrich Repeat element profiling False False +repenrich2 Repeat element profiling using bowtie2 aligner False False +rgrnastar RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper True False +ribowaltz Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data False False +rsem transcript quantification from RNA-Seq data False False +rseqc an RNA-seq quality control package False False +ruvseq Remove Unwanted Variation from RNA-Seq Data False False +salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. True False +sashimi_plot Generates a sashimi plot from bam files. False False +sc3 De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. True False +scanpy scanpy-scripts, command-line wrapper scripts around Scanpy. True False +scanpy Scanpy – Single-Cell Analysis in Python True False +scater De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. True False +scater Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. True False +sccaf SCCAF: Single Cell Clustering Assessment Framework. True False +sceasy Convert scRNA data object between popular formats True False +sceasy Converter between difference single-cell formats True False +schicexplorer scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. True False +scmap De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. True False +scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data True False +scpred De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 True False +seurat De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 True False +seurat Seurat - R toolkit for single cell genomics True False +sinto Sinto single-cell analysis tools True False +slamdunk Slamdunk maps and quantifies SLAMseq reads False False +sleuth Sleuth is a program for differential analysis of RNA-Seq data. False False +snapatac2 SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis True False +spapros Select and evaluate probe sets for targeted spatial transcriptomics. True False +star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR False False +stringtie StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. False False +tophat_fusion_post Wrapper for Tophat-Fusion post step False False +transdecoder TransDecoder finds coding regions within transcripts False False +trinity Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq False False +trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. False False +tximport Wrapper for the Bioconductor package tximport False False +ucsc-cell-browser Python pipeline and Javascript scatter plot library for single-cell datasets True False +umi_tools UMI-tools extract - Extract UMIs from fastq True False +velocyto Velocyto is a library for the analysis of RNA velocity. True False +volcanoplot Tool to create a Volcano Plot True False diff --git a/communities/spoc/resources/tools_wordcloud.png b/communities/spoc/resources/tools_wordcloud.png index 4947046d23ec012488a7e5fdc3be8838fcfb1dfe..237caeb2f4e4a25d4e561c555ec29d4e09b83d3d 100644 GIT binary patch delta 51 zcmbO*pK}5bxhYuc8R;lwl#~<{Tj}fPCYBWB None: def export_tools_to_tsv( - tools: List[Dict], output_fp: str, format_list_col: bool = False, add_usage_stats: bool = False + tools: List[Dict], output_fp: str, format_list_col: bool = False, to_keep_columns: Optional[List[str]] = None ) -> None: """ Export tool metadata to TSV output file @@ -563,42 +563,72 @@ def export_tools_to_tsv( # the Galaxy tools need to be formatted for the add_instances_to_table to work df["Galaxy tool ids"] = shared.format_list_column(df["Galaxy tool ids"]) - # if add_usage_stats: - # df = add_usage_stats_for_all_server(df) + if to_keep_columns is not None: + df = df[to_keep_columns] df.to_csv(output_fp, sep="\t", index=False) +def add_status(tool: Dict, tool_status: Dict) -> None: + """ + Add status to tool + + :param tool: dictionary with tools and their metadata + :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated + """ + name = tool["Galaxy wrapper id"] + tool["Reviewed"] = name in tool_status + if name in tool_status: + tool["To keep"] = tool_status[name]["To keep"] + tool["Deprecated"] = tool_status[name]["Deprecated"] + else: + tool["To keep"] = None + tool["Deprecated"] = None + + def filter_tools( tools: List[Dict], ts_cat: List[str], tool_status: Dict, -) -> tuple: +) -> list: """ - Filter tools for specific ToolShed categories and add information if to keep or to exclude + Filter tools for specific ToolShed categories :param tools: dictionary with tools and their metadata :param ts_cat: list of ToolShed categories to keep in the extraction :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated """ - ts_filtered_tools = [] filtered_tools = [] for tool in tools: # filter ToolShed categories and leave function if not in expected categories if check_categories(tool["ToolShed categories"], ts_cat): - name = tool["Galaxy wrapper id"] - tool["Reviewed"] = name in tool_status - keep = None - deprecated = None - if name in tool_status: - keep = tool_status[name][1] - deprecated = tool_status[name][2] - tool["Deprecated"] = deprecated - if keep: # only add tools that are manually marked as to keep - filtered_tools.append(tool) - tool["To keep"] = keep - ts_filtered_tools.append(tool) - return ts_filtered_tools, filtered_tools + filtered_tools.append(tool) + add_status(tool, tool_status) + return filtered_tools + + +def curate_tools( + tools: List[Dict], + tool_status: Dict, +) -> tuple: + """ + Filter tools for specific ToolShed categories + + :param tools: dictionary with tools and their metadata + :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated + """ + curated_tools = [] + tools_wo_biotools = [] + tools_with_biotools = [] + for tool in tools: + add_status(tool, tool_status) + if tool["To keep"]: # only add tools that are manually marked as to keep + curated_tools.append(tool) + if tool["bio.tool id"] is None: + tools_wo_biotools.append(tool) + else: + tools_with_biotools.append(tool) + return curated_tools, tools_wo_biotools, tools_with_biotools def reduce_ontology_terms(terms: List, ontology: Any) -> List: @@ -609,7 +639,6 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List: :terms: list of terms from that ontology :ontology: Ontology """ - # if list is empty do nothing if not terms: return terms @@ -737,8 +766,8 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: help="Run a small test case using only the repository: https://github.com/TGAC/earlham-galaxytools", ) - # Filter tools - filtertools = subparser.add_parser("filter", help="Filter tools") + # Filter tools based on ToolShed categories + filtertools = subparser.add_parser("filter", help="Filter tools based on ToolShed categories") filtertools.add_argument( "--all", "-a", @@ -746,26 +775,56 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: help="Filepath to JSON with all extracted tools, generated by extractools command", ) filtertools.add_argument( - "--ts-filtered", + "--categories", + "-c", + help="Path to a file with ToolShed category to keep in the extraction (one per line)", + ) + filtertools.add_argument( + "--filtered", + "-f", + required=True, + help="Filepath to JSON with tools filtered based on ToolShed category", + ) + filtertools.add_argument( + "--tsv-filtered", "-t", required=True, help="Filepath to TSV with tools filtered based on ToolShed category", ) filtertools.add_argument( + "--status", + "-s", + help="Path to a TSV file with tool status - at least 3 columns: IDs of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not", + ) + + # Curate tools categories + curatetools = subparser.add_parser("curate", help="Curate tools based on community review") + curatetools.add_argument( "--filtered", "-f", required=True, - help="Filepath to TSV with tools filtered based on ToolShed category and manual curation", + help="Filepath to JSON with tools filtered based on ToolShed category", ) - filtertools.add_argument( - "--categories", + curatetools.add_argument( + "--curated", "-c", - help="Path to a file with ToolShed category to keep in the extraction (one per line)", + required=True, + help="Filepath to TSV with curated tools", ) - filtertools.add_argument( + curatetools.add_argument( + "--wo-biotools", + required=True, + help="Filepath to TSV with tools not linked to bio.tools", + ) + curatetools.add_argument( + "--w-biotools", + required=True, + help="Filepath to TSV with tools linked to bio.tools", + ) + curatetools.add_argument( "--status", "-s", - help="Path to a TSV file with tool status - 3 columns: ToolShed ids of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not", + help="Path to a TSV file with tool status - at least 3 columns: IDs of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not", ) args = parser.parse_args() @@ -783,32 +842,61 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: edam_ontology = get_ontology("https://edamontology.org/EDAM_1.25.owl").load() tools = get_tools(repo_list, edam_ontology) export_tools_to_json(tools, args.all) - export_tools_to_tsv(tools, args.all_tsv, format_list_col=True, add_usage_stats=True) + export_tools_to_tsv(tools, args.all_tsv, format_list_col=True) elif args.command == "filter": with Path(args.all).open() as f: tools = json.load(f) # get categories and tools to exclude categories = shared.read_file(args.categories) + # get status if file provided + if args.status: + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + else: + status = {} + # filter tool lists + filtered_tools = filter_tools(tools, categories, status) + if filtered_tools: + export_tools_to_json(filtered_tools, args.filtered) + export_tools_to_tsv( + filtered_tools, + args.tsv_filtered, + format_list_col=True, + to_keep_columns=["Galaxy wrapper id", "Description", "To keep", "Deprecated"], + ) + else: + # if there are no ts filtered tools + print(f"No tools found for category {args.filtered}") + + elif args.command == "curate": + with Path(args.filtered).open() as f: + tools = json.load(f) try: - status = pd.read_csv(args.status, sep="\t", index_col=0, header=None).to_dict("index") + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") except Exception as ex: print(f"Failed to load tool_status.tsv file with:\n{ex}") print("Not assigning tool status for this community !") status = {} - # filter tool lists - ts_filtered_tools, filtered_tools = filter_tools(tools, categories, status) - - if ts_filtered_tools: - - export_tools_to_tsv(ts_filtered_tools, args.ts_filtered, format_list_col=True) - # if there are no filtered tools return the ts filtered tools - if filtered_tools: - export_tools_to_tsv(filtered_tools, args.filtered, format_list_col=True) - else: - export_tools_to_tsv(ts_filtered_tools, args.filtered, format_list_col=True) - + curated_tools, tools_wo_biotools, tools_with_biotools = curate_tools(tools, status) + if curated_tools: + export_tools_to_tsv( + curated_tools, + args.curated, + format_list_col=True, + ) + export_tools_to_tsv( + tools_wo_biotools, + args.wo_biotools, + format_list_col=True, + to_keep_columns=["Galaxy wrapper id", "Source", "Galaxy wrapper source"], + ) + export_tools_to_tsv( + tools_with_biotools, + args.w_biotools, + format_list_col=True, + to_keep_columns=["Galaxy wrapper id", "bio.tool name", "EDAM operation", "EDAM topic"], + ) else: # if there are no ts filtered tools - print(f"No tools found for category {args.filtered}") + print("No tools left after curation") diff --git a/sources/bin/format_tools.sh b/sources/bin/format_tools.sh index 04c88095..ecf25c2a 100755 --- a/sources/bin/format_tools.sh +++ b/sources/bin/format_tools.sh @@ -1,13 +1,27 @@ #!/usr/bin/env bash -python sources/bin/create_interactive_table.py \ - --input "communities/all/resources/tools.tsv" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/all/resources/tools.html" +if [[ ! -z $1 && $1 == "test" ]]; then + python sources/bin/create_interactive_table.py \ + --input "communities/all/resources/test_tools.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/all/resources/tools.html" -python sources/bin/create_wordcloud.py \ - --input "communities/all/resources/tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ - --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ - --output "communities/all/resources/tools_wordcloud.png" \ \ No newline at end of file + python sources/bin/create_wordcloud.py \ + --input "communities/all/resources/test_tools.tsv" \ + --name-col "Galaxy wrapper id" \ + --stat-col "No. of tool users (5 years) - all main servers" \ + --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ + --output "communities/all/resources/tools_wordcloud.png" +else + python sources/bin/create_interactive_table.py \ + --input "communities/all/resources/tools.tsv" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/all/resources/tools.html" + + python sources/bin/create_wordcloud.py \ + --input "communities/all/resources/tools.tsv" \ + --name-col "Galaxy wrapper id" \ + --stat-col "No. of tool users (5 years) - all main servers" \ + --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ + --output "communities/all/resources/tools_wordcloud.png" +fi; \ No newline at end of file diff --git a/sources/bin/get_community_tools.sh b/sources/bin/get_community_tools.sh index d3eb8dcc..165940b5 100755 --- a/sources/bin/get_community_tools.sh +++ b/sources/bin/get_community_tools.sh @@ -7,13 +7,21 @@ if [[ ! -z $1 && $1 == "test" ]]; then python sources/bin/extract_galaxy_tools.py \ filter \ --all "communities/all/resources/tools.json" \ - --ts-filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv" \ - --filtered "communities/microgalaxy/resources/tools.tsv" \ --categories "communities/microgalaxy/metadata/categories" \ + --tsv-filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv" \ + --filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.json" \ --status "communities/microgalaxy/metadata/tool_status.tsv" + + python sources/bin/extract_galaxy_tools.py \ + curate \ + --filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.json" \ + --status "communities/microgalaxy/metadata/tool_status.tsv" \ + --curated "communities/microgalaxy/resources/curated_tools.tsv" \ + --wo-biotools "communities/microgalaxy/resources/curated_tools_wo_biotools.tsv" \ + --w-biotools "communities/microgalaxy/resources/curated_tools_w_biotools.tsv" python sources/bin/create_interactive_table.py \ - --input "communities/microgalaxy/resources/tools.tsv" \ + --input "communities/microgalaxy/resources/curated_tools.tsv" \ --remove-col "Reviewed" \ --remove-col "To keep" \ --filter-col "To keep" \ @@ -21,7 +29,7 @@ if [[ ! -z $1 && $1 == "test" ]]; then --output "communities/microgalaxy/resources/tools.html" python sources/bin/create_wordcloud.py \ - --input "communities/microgalaxy/resources/tools.tsv" \ + --input "communities/microgalaxy/resources/curated_tools.tsv" \ --name-col "Galaxy wrapper id" \ --stat-col "No. of tool users (5 years) - all main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ @@ -35,31 +43,51 @@ else if [ "$community" != "all" ]; then echo "$community"; - mkdir -p "communities/$community/resources" - python sources/bin/extract_galaxy_tools.py \ - filter \ - --all "communities/all/resources/tools.json" \ - --ts-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ - --filtered "communities/$community/resources/tools.tsv" \ - --categories "communities/$community/metadata/categories" \ - --status "communities/$community/metadata/tool_status.tsv" + if [[ -f "communities/$community/metadata/tool_status.tsv" ]]; then + python sources/bin/extract_galaxy_tools.py \ + filter \ + --all "communities/all/resources/tools.json" \ + --categories "communities/$community/metadata/categories" \ + --tsv-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ + --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" \ + --status "communities/$community/metadata/tool_status.tsv" + + python sources/bin/extract_galaxy_tools.py \ + curate \ + --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" \ + --status "communities/$community/metadata/tool_status.tsv" \ + --curated "communities/$community/resources/curated_tools.tsv" \ + --wo-biotools "communities/$community/resources/curated_tools_wo_biotools.tsv" \ + --w-biotools "communities/$community/resources/curated_tools_w_biotools.tsv" + + if [[ -e "communities/$community/resources/curated_tools.tsv" && -f "communities/$community/resources/curated_tools.tsv" ]]; then + python sources/bin/create_interactive_table.py \ + --input "communities/$community/resources/curated_tools.tsv" \ + --remove-col "Reviewed" \ + --remove-col "To keep" \ + --filter-col "To keep" \ + --template "sources/data/interactive_table_template.html" \ + --output "communities/$community/resources/tools.html" + + python sources/bin/create_wordcloud.py \ + --input "communities/$community/resources/curated_tools.tsv" \ + --name-col "Galaxy wrapper id" \ + --stat-col "No. of tool users (5 years) - all main servers" \ + --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ + --output "communities/$community/resources/tools_wordcloud.png" + fi; - python sources/bin/create_interactive_table.py \ - --input "communities/$community/resources/tools.tsv" \ - --remove-col "Reviewed" \ - --remove-col "To keep" \ - --filter-col "To keep" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/$community/resources/tools.html" + else + python sources/bin/extract_galaxy_tools.py \ + filter \ + --all "communities/all/resources/tools.json" \ + --categories "communities/$community/metadata/categories" \ + --tsv-filtered "communities/$community/resources/tools_filtered_by_ts_categories.tsv" \ + --filtered "communities/$community/resources/tools_filtered_by_ts_categories.json" - python sources/bin/create_wordcloud.py \ - --input "communities/$community/resources/tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ - --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ - --output "communities/$community/resources/tools_wordcloud.png" + fi; fi; fi; done From f8e77107c83a1377c4255657dcd31fc8886d1ad6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 6 Nov 2024 18:51:13 +0100 Subject: [PATCH 8/9] Rename tool columns and add documentation (#222) --- README.md | 40 +- communities/all/resources/test_tools.json | 786 ++++++++++------------ communities/all/resources/test_tools.tsv | 13 +- sources/bin/extract_galaxy_tools.py | 188 +++--- sources/bin/format_tools.sh | 8 +- sources/bin/get_community_tools.sh | 28 +- 6 files changed, 513 insertions(+), 550 deletions(-) diff --git a/README.md b/README.md index 992a829f..2d19b61d 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,43 @@ Galaxy Codex Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community. -This repository stores the sources to build this catalog. The catalog is automatically updated every week. - +This repository stores the sources to build this catalog and its content. The catalog is automatically updated every week. Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**. + +# Catalog content + +## Tool table + +Column | Description +--- | --- +Suite ID | ID of Galaxy suite +Tool IDs | List of Galaxy tool IDs +Description | Description of the suite +Homepage | Homepage for tool +Suite version | Version of the Galaxy suite +Suite Conda package | Conda package used as requirement for the suite +Latest suite conda package version | Latest Conda package version on anaconda +Suite version status | Update status derived by comparing the suite version to the latest conda package version +ToolShed categories | +EDAM operations | EDAM operations extracted using bio.tools +EDAM reduced operations | EDAM operations where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed +EDAM topics | EDAM topics extracted using bio.tools +EDAM reduced topics | EDAM topics where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed +Suite owner | Owner of the Galaxy suite +Suite source | Path to the Galaxy suite +bio.tools ID | ID of the bio.tools entry corresponding to the tool +bio.tools name | Name of the bio.tools entry corresponding to the tool +bio.tools description | Description in bio.tools entry corresponding to the tool +bii ID | ID of BII entry corresponding to the tool +Number of tools available on ... | Number of tools available on given Galaxy server +Suite users (last 5 years) on ... | Number of users of the suite in the last 5 years on given Galaxy server +Suite users on ... | Number of users of the suite on given Galaxy server +Suite runs (last 5 years) on ... | Number of runs of the suite tools in the last 5 years on given Galaxy server +Suite runs on ... | Number of runs of the suite tools on given Galaxy server +Suite users (last 5 years) on main servers | Number of users of the suite in the last 5 years on all UseGalaxy servers +Suite users on main servers | Number of users of the suite on all UseGalaxy servers +Suite runs (last 5 years) on main servers | Number of runs of the suite tools in the last 5 years on all UseGalaxy servers +Suite runs on main servers | Number of runs of the suite tools on all UseGalaxy servers +Deprecated | Deprecation status after review by a domain expert +To keep | Status to add to a community after review by a domain expert \ No newline at end of file diff --git a/communities/all/resources/test_tools.json b/communities/all/resources/test_tools.json index 0bad9a6f..c580a197 100644 --- a/communities/all/resources/test_tools.json +++ b/communities/all/resources/test_tools.json @@ -1,391 +1,361 @@ [ { - "Galaxy wrapper id": "2d_auto_threshold", - "Galaxy tool ids": [ + "Suite ID": "2d_auto_threshold", + "Tool IDs": [ "ip_threshold" ], "Description": "Automatic thresholding", - "bio.tool id": "scikit-image", - "bio.tool ids": [ - "scikit-image" + "Suite first commit date": "2024-03-01", + "Homepage": "https://github.com/bmcv", + "Suite version": "0.0.6-2", + "Suite conda package": "scikit-image", + "Latest suite conda package version": null, + "Suite version status": "To update", + "ToolShed categories": [ + "Imaging" ], - "biii": "scikit-image", - "bio.tool name": "scikit-image", - "bio.tool description": "Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.", - "EDAM operation": [ + "EDAM operations": [ "Image analysis", "Image annotation", "Visualisation", "Data handling" ], - "EDAM topic": [ - "Imaging", - "Software engineering", - "Literature and language" - ], - "Status": "To update", - "Source": "https://github.com/bmcv", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "2d_auto_threshold", - "Date of first commit of the suite": "2024-03-01", - "Galaxy wrapper owner": "imgteam", - "Galaxy wrapper source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/", - "Galaxy wrapper parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold", - "Galaxy wrapper version": "0.0.6-2", - "Conda id": "scikit-image", - "Conda version": null, - "EDAM operation (no superclasses)": [ + "EDAM reduced operations": [ "Image analysis", "Image annotation", "Visualisation", "Data handling" ], - "EDAM topic (no superclasses)": [ + "EDAM topics": [ + "Imaging", + "Software engineering", + "Literature and language" + ], + "EDAM reduced topics": [ "Imaging", "Software engineering", "Literature and language" ], - "Available on UseGalaxy.org (Main)": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.fr": 0, - "Tools available on UseGalaxy.org (Main)": 0, - "Tools available on UseGalaxy.org.au": 1, - "Tools available on UseGalaxy.eu": 1, - "Tools available on UseGalaxy.fr": 0, - "Tools available on APOSTL": 0, - "Tools available on BF2I-MAP": 0, - "Tools available on BioBix": 0, - "Tools available on CIRM-CFBP": 0, - "Tools available on Center for Phage Technology (CPT)": 0, - "Tools available on ChemFlow": 0, - "Tools available on Coloc-stats": 0, - "Tools available on CoralSNP": 0, - "Tools available on CropGalaxy": 0, - "Tools available on Dintor": 0, - "Tools available on FreeBioinfo": 0, - "Tools available on GASLINI": 0, - "Tools available on Galaxy@AuBi": 0, - "Tools available on Galaxy@Pasteur": 0, - "Tools available on GalaxyTrakr": 0, - "Tools available on Genomic Hyperbrowser": 0, - "Tools available on GigaGalaxy": 0, - "Tools available on HyPhy HIV NGS Tools": 0, - "Tools available on IPK Galaxy Blast Suite": 0, - "Tools available on ImmPort Galaxy": 0, - "Tools available on InteractoMIX": 0, - "Tools available on MISSISSIPPI": 0, - "Tools available on Mandoiu Lab": 0, - "Tools available on MiModD NacreousMap": 0, - "Tools available on Oqtans": 0, - "Tools available on Palfinder": 0, - "Tools available on PepSimili": 0, - "Tools available on PhagePromotor": 0, - "Tools available on UseGalaxy.be": 1, - "Tools available on UseGalaxy.cz": 1, - "Tools available on UseGalaxy.no": 1, - "Tools available on Viral Variant Visualizer (VVV)": 0, - "No. of tool users (5 years) (usegalaxy.eu)": 1434, - "No. of tool users (all time) (usegalaxy.eu)": 6746, - "Tool usage (5 years) (usegalaxy.eu)": 120, - "Tool usage (all time) (usegalaxy.eu)": 122, - "No. of tool users (5 years) (usegalaxy.org)": 0, - "No. of tool users (all time) (usegalaxy.org)": 0, - "Tool usage (5 years) (usegalaxy.org)": 0, - "Tool usage (all time) (usegalaxy.org)": 0, - "No. of tool users (5 years) (usegalaxy.org.au)": 305, - "No. of tool users (all time) (usegalaxy.org.au)": 305, - "Tool usage (5 years) (usegalaxy.org.au)": 11, - "Tool usage (all time) (usegalaxy.org.au)": 11, - "No. of tool users (5 years) - all main servers": 1739, - "No. of tool users (all time) - all main servers": 7051, - "Tool usage (5 years) - all main servers": 131, - "Tool usage (all time) - all main servers": 133 + "Suite owner": "imgteam", + "Suite source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/", + "Suite parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold", + "bio.tool ID": "scikit-image", + "bio.tool name": "scikit-image", + "bio.tool description": "Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.", + "biii ID": "scikit-image", + "Number of tools on UseGalaxy.org (Main)": 1, + "Number of tools on UseGalaxy.org.au": 1, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 1, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 0, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MiModD NacreousMap": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PepSimili": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 1, + "Number of tools on UseGalaxy.cz": 1, + "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 120, + "Suite users (usegalaxy.eu)": 122, + "Suite runs (last 5 years) (usegalaxy.eu)": 1434, + "Suite runs (usegalaxy.eu)": 6746, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 11, + "Suite users (usegalaxy.org.au)": 11, + "Suite runs (last 5 years) (usegalaxy.org.au)": 305, + "Suite runs (usegalaxy.org.au)": 305, + "Suite users (last 5 years) on main servers": 131, + "Suite users on main servers": 395, + "Suite runs (last 5 years) on main servers": 1739, + "Suite runs on main servers": 10529 }, { - "Galaxy wrapper id": "abritamr", - "Galaxy tool ids": [ + "Suite ID": "abritamr", + "Tool IDs": [ "abritamr" ], "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://zenodo.org/record/7370628", + "Suite first commit date": "2024-03-01", + "Homepage": "https://zenodo.org/record/7370628", + "Suite version": "1.0.14", + "Suite conda package": "abritamr", + "Latest suite conda package version": "1.0.19", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], - "ToolShed id": "abritamr", - "Date of first commit of the suite": "2024-03-01", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", - "Galaxy wrapper parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr", - "Galaxy wrapper version": "1.0.14", - "Conda id": "abritamr", - "Conda version": "1.0.19", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org (Main)": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.fr": 0, - "Tools available on UseGalaxy.org (Main)": 0, - "Tools available on UseGalaxy.org.au": 0, - "Tools available on UseGalaxy.eu": 1, - "Tools available on UseGalaxy.fr": 0, - "Tools available on APOSTL": 0, - "Tools available on BF2I-MAP": 0, - "Tools available on BioBix": 0, - "Tools available on CIRM-CFBP": 0, - "Tools available on Center for Phage Technology (CPT)": 0, - "Tools available on ChemFlow": 0, - "Tools available on Coloc-stats": 0, - "Tools available on CoralSNP": 0, - "Tools available on CropGalaxy": 0, - "Tools available on Dintor": 0, - "Tools available on FreeBioinfo": 0, - "Tools available on GASLINI": 0, - "Tools available on Galaxy@AuBi": 0, - "Tools available on Galaxy@Pasteur": 0, - "Tools available on GalaxyTrakr": 0, - "Tools available on Genomic Hyperbrowser": 0, - "Tools available on GigaGalaxy": 0, - "Tools available on HyPhy HIV NGS Tools": 0, - "Tools available on IPK Galaxy Blast Suite": 0, - "Tools available on ImmPort Galaxy": 0, - "Tools available on InteractoMIX": 0, - "Tools available on MISSISSIPPI": 0, - "Tools available on Mandoiu Lab": 0, - "Tools available on MiModD NacreousMap": 0, - "Tools available on Oqtans": 0, - "Tools available on Palfinder": 0, - "Tools available on PepSimili": 0, - "Tools available on PhagePromotor": 0, - "Tools available on UseGalaxy.be": 0, - "Tools available on UseGalaxy.cz": 0, - "Tools available on UseGalaxy.no": 0, - "Tools available on Viral Variant Visualizer (VVV)": 0, - "No. of tool users (5 years) (usegalaxy.eu)": 1139, - "No. of tool users (all time) (usegalaxy.eu)": 1139, - "Tool usage (5 years) (usegalaxy.eu)": 109, - "Tool usage (all time) (usegalaxy.eu)": 109, - "No. of tool users (5 years) (usegalaxy.org)": 0, - "No. of tool users (all time) (usegalaxy.org)": 0, - "Tool usage (5 years) (usegalaxy.org)": 0, - "Tool usage (all time) (usegalaxy.org)": 0, - "No. of tool users (5 years) (usegalaxy.org.au)": 0, - "No. of tool users (all time) (usegalaxy.org.au)": 0, - "Tool usage (5 years) (usegalaxy.org.au)": 0, - "Tool usage (all time) (usegalaxy.org.au)": 0, - "No. of tool users (5 years) - all main servers": 1139, - "No. of tool users (all time) - all main servers": 1139, - "Tool usage (5 years) - all main servers": 109, - "Tool usage (all time) - all main servers": 109 + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": "iuc", + "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", + "Suite parsed folder": "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr", + "bio.tool ID": null, + "bio.tool name": null, + "bio.tool description": null, + "biii ID": null, + "Number of tools on UseGalaxy.org (Main)": 0, + "Number of tools on UseGalaxy.org.au": 0, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 0, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 0, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MiModD NacreousMap": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PepSimili": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 0, + "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 109, + "Suite users (usegalaxy.eu)": 109, + "Suite runs (last 5 years) (usegalaxy.eu)": 1139, + "Suite runs (usegalaxy.eu)": 1139, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 0, + "Suite users (usegalaxy.org.au)": 0, + "Suite runs (last 5 years) (usegalaxy.org.au)": 0, + "Suite runs (usegalaxy.org.au)": 0, + "Suite users (last 5 years) on main servers": 109, + "Suite users on main servers": 327, + "Suite runs (last 5 years) on main servers": 1139, + "Suite runs on main servers": 3417 }, { - "Galaxy wrapper id": "aldex2", - "Galaxy tool ids": [ + "Suite ID": "aldex2", + "Tool IDs": [ "aldex2" ], "Description": "Performs analysis Of differential abundance taking sample variation into account", - "bio.tool id": "aldex2", - "bio.tool ids": [ - "aldex2" + "Suite first commit date": "2024-03-01", + "Homepage": "https://github.com/ggloor/ALDEx_bioc", + "Suite version": "1.26.0", + "Suite conda package": "bioconductor-aldex2", + "Latest suite conda package version": "1.34.0", + "Suite version status": "To update", + "ToolShed categories": [ + "Metagenomics" ], - "biii": null, - "bio.tool name": "ALDEx2", - "bio.tool description": "A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. 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Additional contigs can be provided and can be used as long reads.", + "biii ID": null, + "Number of tools on UseGalaxy.org (Main)": 9, + "Number of tools on UseGalaxy.org.au": 9, + "Number of tools on UseGalaxy.eu": 9, + "Number of tools on UseGalaxy.fr": 9, + "Number of tools on APOSTL": 0, + "Number of tools on BF2I-MAP": 0, + "Number of tools on BioBix": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Center for Phage Technology (CPT)": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on CoralSNP": 0, + "Number of tools on CropGalaxy": 0, + "Number of tools on Dintor": 0, + "Number of tools on FreeBioinfo": 0, + "Number of tools on GASLINI": 0, + "Number of tools on Galaxy@AuBi": 1, + "Number of tools on Galaxy@Pasteur": 3, + "Number of tools on GalaxyTrakr": 8, + "Number of tools on Genomic Hyperbrowser": 0, + "Number of tools on GigaGalaxy": 0, + "Number of tools on HyPhy HIV NGS Tools": 2, + "Number of tools on IPK 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(usegalaxy.org.au)": 6653, + "Suite runs (last 5 years) (usegalaxy.org.au)": 54067, + "Suite runs (usegalaxy.org.au)": 61541, + "Suite users (last 5 years) on main servers": 28813, + "Suite users on main servers": 87595, + "Suite runs (last 5 years) on main servers": 257254, + "Suite runs on main servers": 783637 } ] \ No newline at end of file diff --git a/communities/all/resources/test_tools.tsv b/communities/all/resources/test_tools.tsv index f60a80e2..7f68d13f 100644 --- a/communities/all/resources/test_tools.tsv +++ b/communities/all/resources/test_tools.tsv @@ -1,7 +1,6 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on BF2I-MAP Tools available on BioBix Tools available on CIRM-CFBP Tools available on Center for Phage Technology (CPT) Tools available on ChemFlow Tools available on Coloc-stats Tools available on CoralSNP Tools available on CropGalaxy Tools available on Dintor Tools available on FreeBioinfo Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) -2d_auto_threshold ip_threshold Automatic thresholding scikit-image scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold 2024-03-01 imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold 0.0.6-2 scikit-image Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1434 6746 120 122 0 0 0 0 305 305 11 11 -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes To update https://zenodo.org/record/7370628 Sequence Analysis abritamr 2024-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 1.0.14 abritamr 1.0.19 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1139 1139 109 109 0 0 0 0 0 0 0 0 -aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2024-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0 -fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers To update https://github.com/OpenGene/fastp Sequence Analysis fastp 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242 -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades metaplasmidspades, rnaspades, metaviralspades, spades, rnaviralspades, plasmidspades, coronaspades, biosyntheticspades, metaspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2024-03-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 0 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653 - +Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on BF2I-MAP Number of tools on BioBix Number of tools on CIRM-CFBP Number of tools on Center for Phage Technology (CPT) Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on HyPhy HIV NGS Tools Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) on main servers Suite users on main servers Suite runs (last 5 years) on main servers Suite runs on main servers +2d_auto_threshold ip_threshold Automatic thresholding 2024-03-01 https://github.com/bmcv 0.0.6-2 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 120 122 1434 6746 0 0 0 0 11 11 305 305 131 395 1739 10529 +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes 2024-03-01 https://zenodo.org/record/7370628 1.0.14 abritamr 1.0.19 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 109 109 1139 1139 0 0 0 0 0 0 0 0 109 327 1139 3417 +aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account 2024-03-01 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.34.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 262 262 0 0 0 0 0 0 0 0 36 108 262 786 +fastp fastp Fast all-in-one preprocessing for FASTQ files 2024-03-11 https://github.com/OpenGene/fastp fastp 0.23.4 To update Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 6847 6909 1126086 1127111 10722 10722 422259 422259 2242 2242 76462 76462 19811 59495 1624807 4875446 +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2024-03-12 https://github.com/ablab/spades 3.15.5 spades 4.0.0 To update Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8209 8526 82716 87113 14787 14790 120471 120475 5817 6653 54067 61541 28813 87595 257254 783637 diff --git a/sources/bin/extract_galaxy_tools.py b/sources/bin/extract_galaxy_tools.py index 01279a4c..47a015f4 100644 --- a/sources/bin/extract_galaxy_tools.py +++ b/sources/bin/extract_galaxy_tools.py @@ -40,34 +40,27 @@ public_servers = project_path.joinpath("data", "available_public_servers.csv") -GALAXY_TOOL_STATS = { - # EU - "No. of tool users (5 years) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_usage_5y_until_2024.08.31.csv"), - "No. of tool users (all time) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_usage_until_2024.08.31.csv"), - "Tool usage (5 years) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.eu)": usage_stats_path.joinpath("eu/tool_users_until_2024.08.31.csv"), - # ORG - "No. of tool users (5 years) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_usage_5y_until_2024.08.31.csv"), - "No. of tool users (all time) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_usage_until_2024.08.31.csv"), - "Tool usage (5 years) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.org)": usage_stats_path.joinpath("org/tool_users_until_2024.08.31.csv"), - # AU - "No. of tool users (5 years) (usegalaxy.org.au)": usage_stats_path.joinpath( - "org.au/tool_usage_5y_until_2024.08.31.csv" - ), - "No. of tool users (all time) (usegalaxy.org.au)": usage_stats_path.joinpath( - "org.au/tool_usage_until_2024.08.31.csv" - ), - "Tool usage (5 years) (usegalaxy.org.au)": usage_stats_path.joinpath("org.au/tool_users_5y_until_2024.08.31.csv"), - "Tool usage (all time) (usegalaxy.org.au)": usage_stats_path.joinpath("org.au/tool_users_until_2024.08.31.csv"), -} +GALAXY_TOOL_STATS = {} +for server in ["eu", "org", "org.au"]: + GALAXY_TOOL_STATS[f"Suite users (last 5 years) (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_users_5y_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite users (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_users_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite runs (last 5 years) (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_usage_5y_until_2024.08.31.csv" + ) + GALAXY_TOOL_STATS[f"Suite runs (usegalaxy.{ server })"] = usage_stats_path.joinpath( + f"{ server }/tool_usage_until_2024.08.31.csv" + ) # all columns that contain the text will be summed up to a new column with summed up stats GALAXY_TOOL_STATS_SUM = [ - "No. of tool users (5 years)", - "No. of tool users (all time)", - "Tool usage (5 years)", - "Tool usage (all time)", + "Suite users (last 5 years)", + "Suite users", + "Suite runs (last 5 years)", + "Suite runs", ] # load the configs globally @@ -100,15 +93,15 @@ def get_tool_stats_from_stats_file(tool_stats_df: pd.DataFrame, tool_ids: List[s """ # extract tool id - tool_stats_df["Galaxy wrapper id"] = tool_stats_df["tool_name"].apply(get_last_url_position) - # print(tool_stats_df["Galaxy wrapper id"].to_list()) + tool_stats_df["Suite ID"] = tool_stats_df["tool_name"].apply(get_last_url_position) + # print(tool_stats_df["Suite ID"].to_list()) agg_count = 0 for tool_id in tool_ids: - if tool_id in tool_stats_df["Galaxy wrapper id"].to_list(): + if tool_id in tool_stats_df["Suite ID"].to_list(): # get stats of the tool for all versions - counts = tool_stats_df.loc[(tool_stats_df["Galaxy wrapper id"] == tool_id), "count"] + counts = tool_stats_df.loc[(tool_stats_df["Suite ID"] == tool_id), "count"] agg_versions = counts.sum() # aggregate all counts for all tools in the suite @@ -272,29 +265,28 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, if tool.type != "dir": return None - # the folder of the tool is used as Galaxy wrapper id (maybe rather use the .shed.yml name) - metadata = { - "Galaxy wrapper id": tool.name, - "Galaxy tool ids": [], + metadata: dict = { + "Suite ID": None, + "Tool IDs": [], "Description": None, - "bio.tool id": None, - "bio.tool ids": set(), # keep track of multi IDs - "biii": None, + "Suite first commit date": None, + "Homepage": None, + "Suite version": None, + "Suite conda package": None, + "Latest suite conda package version": None, + "Suite version status": "To update", + "ToolShed categories": [], + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": None, + "Suite source": None, # this is what it written in the .shed.yml + "Suite parsed folder": None, # this is the actual parsed file + "bio.tool ID": None, "bio.tool name": None, "bio.tool description": None, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": None, - "ToolShed categories": [], - "ToolShed id": None, - "Date of first commit of the suite": None, - "Galaxy wrapper owner": None, - "Galaxy wrapper source": None, # this is what it written in the .shed.yml - "Galaxy wrapper parsed folder": None, # this is the actual parsed file - "Galaxy wrapper version": None, - "Conda id": None, - "Conda version": None, + "biii ID": None, } # extract .shed.yml information and check macros.xml try: @@ -310,11 +302,11 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, metadata["Description"] = get_shed_attribute("long_description", yaml_content, None) if metadata["Description"] is not None: metadata["Description"] = metadata["Description"].replace("\n", "") - metadata["ToolShed id"] = get_shed_attribute("name", yaml_content, None) - metadata["Galaxy wrapper owner"] = get_shed_attribute("owner", yaml_content, None) - metadata["Galaxy wrapper source"] = get_shed_attribute("remote_repository_url", yaml_content, None) + metadata["Suite ID"] = get_shed_attribute("name", yaml_content, None) + metadata["Suite owner"] = get_shed_attribute("owner", yaml_content, None) + metadata["Suite source"] = get_shed_attribute("remote_repository_url", yaml_content, None) if "homepage_url" in yaml_content: - metadata["Source"] = yaml_content["homepage_url"] + metadata["Homepage"] = yaml_content["homepage_url"] metadata["ToolShed categories"] = get_shed_attribute("categories", yaml_content, []) if metadata["ToolShed categories"] is None: metadata["ToolShed categories"] = [] @@ -324,10 +316,10 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, assert isinstance(file_list, list) # store the github location where the folder was parsed - metadata["Galaxy wrapper parsed folder"] = tool.html_url + metadata["Suite parsed folder"] = tool.html_url # get the first commit date - metadata["Date of first commit of the suite"] = shared.get_first_commit_for_folder(tool, repo) + metadata["Suite first commit date"] = shared.get_first_commit_for_folder(tool, repo) # find and parse macro file for file in file_list: @@ -337,18 +329,17 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, for child in root: if "name" in child.attrib: if child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@": - metadata["Galaxy wrapper version"] = child.text + metadata["Suite version"] = child.text elif child.attrib["name"] == "requirements": - metadata["Conda id"] = get_conda_package(child) + metadata["Suite conda package"] = get_conda_package(child) # bio.tools biotools = get_xref(child, attrib_type="bio.tools") if biotools is not None: - metadata["bio.tool id"] = biotools - metadata["bio.tool ids"].add(biotools) + metadata["bio.tool ID"] = biotools # biii biii = get_xref(child, attrib_type="biii") if biii is not None: - metadata["biii"] = biii + metadata["biii ID"] = biii # parse XML file and get meta data from there for file in file_list: @@ -360,11 +351,11 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, print(traceback.format_exc()) else: # version - if metadata["Galaxy wrapper version"] is None: + if metadata["Suite version"] is None: if "version" in root.attrib: version = root.attrib["version"] if "VERSION@" not in version: - metadata["Galaxy wrapper version"] = version + metadata["Suite version"] = version else: macros = root.find("macros") if macros is not None: @@ -372,52 +363,51 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, if "name" in child.attrib and ( child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@" ): - metadata["Galaxy wrapper version"] = child.text + metadata["Suite version"] = child.text # bio.tools biotools = get_xref(root, attrib_type="bio.tools") if biotools is not None: - metadata["bio.tool id"] = biotools - metadata["bio.tool ids"].add(biotools) + metadata["bio.tool ID"] = biotools # biii - if metadata["biii"] is None: + if metadata["biii ID"] is None: biii = get_xref(root, attrib_type="biii") if biii is not None: - metadata["biii"] = biii + metadata["biii ID"] = biii # conda package - if metadata["Conda id"] is None: + if metadata["Suite conda package"] is None: reqs = get_conda_package(root) if reqs is not None: - metadata["Conda id"] = reqs + metadata["Suite conda package"] = reqs # tool ids if "id" in root.attrib: - metadata["Galaxy tool ids"].append(root.attrib["id"]) + metadata["Tool IDs"].append(root.attrib["id"]) # get latest conda version and compare to the wrapper version - if metadata["Conda id"] is not None: - r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Conda id"]}') + if metadata["Suite conda package"] is not None: + r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Suite conda package"]}') if r.status_code == requests.codes.ok: conda_info = r.json() if "latest_version" in conda_info: - metadata["Conda version"] = conda_info["latest_version"] - if metadata["Conda version"] == metadata["Galaxy wrapper version"]: - metadata["Status"] = "Up-to-date" + metadata["Latest suite conda package version"] = conda_info["latest_version"] + if metadata["Latest suite conda package version"] == metadata["Suite version"]: + metadata["Suite version status"] = "Up-to-date" # get bio.tool information - if metadata["bio.tool id"] is not None: - r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool id"]}/?format=json') + if metadata["bio.tool ID"] is not None: + r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool ID"]}/?format=json') if r.status_code == requests.codes.ok: biotool_info = r.json() if "function" in biotool_info: for func in biotool_info["function"]: if "operation" in func: for op in func["operation"]: - metadata["EDAM operation"].append(op["term"]) + metadata["EDAM operations"].append(op["term"]) if "topic" in biotool_info: for t in biotool_info["topic"]: - metadata["EDAM topic"].append(t["term"]) + metadata["EDAM topics"].append(t["term"]) if "name" in biotool_info: metadata["bio.tool name"] = biotool_info["name"] if "description" in biotool_info: @@ -549,19 +539,17 @@ def export_tools_to_tsv( :param format_list_col: boolean indicating if list columns should be formatting """ - df = pd.DataFrame(tools).sort_values("Galaxy wrapper id") + df = pd.DataFrame(tools).sort_values("Suite ID") if format_list_col: df["ToolShed categories"] = shared.format_list_column(df["ToolShed categories"]) - df["EDAM operation"] = shared.format_list_column(df["EDAM operation"]) - df["EDAM topic"] = shared.format_list_column(df["EDAM topic"]) + df["EDAM operations"] = shared.format_list_column(df["EDAM operations"]) + df["EDAM topics"] = shared.format_list_column(df["EDAM topics"]) - df["EDAM operation (no superclasses)"] = shared.format_list_column(df["EDAM operation (no superclasses)"]) - df["EDAM topic (no superclasses)"] = shared.format_list_column(df["EDAM topic (no superclasses)"]) - - df["bio.tool ids"] = shared.format_list_column(df["bio.tool ids"]) + df["EDAM reduced operations"] = shared.format_list_column(df["EDAM reduced operations"]) + df["EDAM reduced topics"] = shared.format_list_column(df["EDAM reduced topics"]) # the Galaxy tools need to be formatted for the add_instances_to_table to work - df["Galaxy tool ids"] = shared.format_list_column(df["Galaxy tool ids"]) + df["Tool IDs"] = shared.format_list_column(df["Tool IDs"]) if to_keep_columns is not None: df = df[to_keep_columns] @@ -576,8 +564,7 @@ def add_status(tool: Dict, tool_status: Dict) -> None: :param tool: dictionary with tools and their metadata :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated """ - name = tool["Galaxy wrapper id"] - tool["Reviewed"] = name in tool_status + name = tool["Suite ID"] if name in tool_status: tool["To keep"] = tool_status[name]["To keep"] tool["Deprecated"] = tool_status[name]["Deprecated"] @@ -624,7 +611,7 @@ def curate_tools( add_status(tool, tool_status) if tool["To keep"]: # only add tools that are manually marked as to keep curated_tools.append(tool) - if tool["bio.tool id"] is None: + if tool["bio.tool ID"] is None: tools_wo_biotools.append(tool) else: tools_with_biotools.append(tool) @@ -695,15 +682,12 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: # add additional information to tools for tool in tools: # add EDAM terms without superclass - tool["EDAM operation (no superclasses)"] = reduce_ontology_terms(tool["EDAM operation"], ontology=edam_ontology) - tool["EDAM topic (no superclasses)"] = reduce_ontology_terms(tool["EDAM topic"], ontology=edam_ontology) + tool["EDAM reduced operations"] = reduce_ontology_terms(tool["EDAM operations"], ontology=edam_ontology) + tool["EDAM reduced topics"] = reduce_ontology_terms(tool["EDAM topics"], ontology=edam_ontology) # add availability for UseGalaxy servers for name, url in USEGALAXY_SERVER_URLS.items(): - tool[f"Available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) - # add availability for all UseGalaxy servers - for name, url in USEGALAXY_SERVER_URLS.items(): - tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) # add all other available servers public_servers_df = pd.read_csv(public_servers, sep="\t") @@ -715,12 +699,12 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: ]: # do not query UseGalaxy servers again url = row["url"] - tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) # add tool stats for name, path in GALAXY_TOOL_STATS.items(): tool_stats_df = pd.read_csv(path) - tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Galaxy tool ids"]) + tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Tool IDs"]) # sum up tool stats for names_to_match in GALAXY_TOOL_STATS_SUM: @@ -728,7 +712,7 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: for col_name in tool.keys(): if names_to_match in col_name: summed_stat += tool[col_name] - tool[f"{names_to_match} - all main servers"] = summed_stat + tool[f"{names_to_match} on main servers"] = summed_stat return tools @@ -862,7 +846,7 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: filtered_tools, args.tsv_filtered, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "Description", "To keep", "Deprecated"], + to_keep_columns=["Suite ID", "Description", "To keep", "Deprecated"], ) else: # if there are no ts filtered tools @@ -889,13 +873,13 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]: tools_wo_biotools, args.wo_biotools, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "Source", "Galaxy wrapper source"], + to_keep_columns=["Suite ID", "Homepage", "Suite source"], ) export_tools_to_tsv( tools_with_biotools, args.w_biotools, format_list_col=True, - to_keep_columns=["Galaxy wrapper id", "bio.tool name", "EDAM operation", "EDAM topic"], + to_keep_columns=["Suite ID", "bio.tool name", "EDAM operations", "EDAM topics"], ) else: # if there are no ts filtered tools diff --git a/sources/bin/format_tools.sh b/sources/bin/format_tools.sh index ecf25c2a..6514c887 100755 --- a/sources/bin/format_tools.sh +++ b/sources/bin/format_tools.sh @@ -8,8 +8,8 @@ if [[ ! -z $1 && $1 == "test" ]]; then python sources/bin/create_wordcloud.py \ --input "communities/all/resources/test_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite users on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/all/resources/tools_wordcloud.png" else @@ -20,8 +20,8 @@ else python sources/bin/create_wordcloud.py \ --input "communities/all/resources/tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite users on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/all/resources/tools_wordcloud.png" fi; \ No newline at end of file diff --git a/sources/bin/get_community_tools.sh b/sources/bin/get_community_tools.sh index 165940b5..4b2772c4 100755 --- a/sources/bin/get_community_tools.sh +++ b/sources/bin/get_community_tools.sh @@ -6,7 +6,7 @@ set -e if [[ ! -z $1 && $1 == "test" ]]; then python sources/bin/extract_galaxy_tools.py \ filter \ - --all "communities/all/resources/tools.json" \ + --all "communities/all/resources/test_tools.json" \ --categories "communities/microgalaxy/metadata/categories" \ --tsv-filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv" \ --filtered "communities/microgalaxy/resources/tools_filtered_by_ts_categories.json" \ @@ -20,18 +20,10 @@ if [[ ! -z $1 && $1 == "test" ]]; then --wo-biotools "communities/microgalaxy/resources/curated_tools_wo_biotools.tsv" \ --w-biotools "communities/microgalaxy/resources/curated_tools_w_biotools.tsv" - python sources/bin/create_interactive_table.py \ - --input "communities/microgalaxy/resources/curated_tools.tsv" \ - --remove-col "Reviewed" \ - --remove-col "To keep" \ - --filter-col "To keep" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/microgalaxy/resources/tools.html" - python sources/bin/create_wordcloud.py \ --input "communities/microgalaxy/resources/curated_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite runs (last 5 years) on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/microgalaxy/resources/tools_wordcloud.png" @@ -62,19 +54,11 @@ else --wo-biotools "communities/$community/resources/curated_tools_wo_biotools.tsv" \ --w-biotools "communities/$community/resources/curated_tools_w_biotools.tsv" - if [[ -e "communities/$community/resources/curated_tools.tsv" && -f "communities/$community/resources/curated_tools.tsv" ]]; then - python sources/bin/create_interactive_table.py \ - --input "communities/$community/resources/curated_tools.tsv" \ - --remove-col "Reviewed" \ - --remove-col "To keep" \ - --filter-col "To keep" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/$community/resources/tools.html" - + if [[ -e "communities/$community/resources/curated_tools.tsv" && -f "communities/$community/resources/curated_tools.tsv" ]]; then python sources/bin/create_wordcloud.py \ --input "communities/$community/resources/curated_tools.tsv" \ - --name-col "Galaxy wrapper id" \ - --stat-col "No. of tool users (5 years) - all main servers" \ + --name-col "Suite ID" \ + --stat-col "Suite runs (last 5 years) on main servers" \ --wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \ --output "communities/$community/resources/tools_wordcloud.png" fi; From 1ba01713bfbb3e16875bb538acecf9e6bc170458 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 6 Nov 2024 19:02:18 +0100 Subject: [PATCH 9/9] combine CI and move docs --- .github/workflows/lint.yaml | 29 +++++++++++++++++-- .github/workflows/run_unittests.yaml | 26 ----------------- sources/README.md | 7 +++++ sources/bin/tests/readme.md | 6 ---- .../tests/test_extract_galaxy_workflows.py | 7 ++--- 5 files changed, 36 insertions(+), 39 deletions(-) delete mode 100644 .github/workflows/run_unittests.yaml delete mode 100644 sources/bin/tests/readme.md diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 1170c71c..333198f7 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -1,8 +1,16 @@ -name: Lint -on: [push, pull_request] +name: Code best practice and unittesting + +on: + pull_request: + branches: + - main + paths: + - 'bin/**' # This will trigger the workflow only if files in the 'bin' folder are modified. + concurrency: group: lint-${{ github.ref }} cancel-in-progress: true + jobs: lint: runs-on: ubuntu-latest @@ -15,3 +23,20 @@ jobs: run: python -m pip install 'tox>=1.8.0' - name: Lint run: tox -e lint + + unittest: + runs-on: ubuntu-20.04 + strategy: + matrix: + python-version: ['3.11'] + steps: + - name: Checkout + uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install requirements + run: python -m pip install -r requirements.txt + - name: Run unittests + run: | + PYTHONPATH=bin python -m unittest discover -s bin/tests \ No newline at end of file diff --git a/.github/workflows/run_unittests.yaml b/.github/workflows/run_unittests.yaml deleted file mode 100644 index 132d5adb..00000000 --- a/.github/workflows/run_unittests.yaml +++ /dev/null @@ -1,26 +0,0 @@ -name: Run tests - -on: - pull_request: - branches: - - main - paths: - - 'bin/**' # This will trigger the workflow only if files in the 'bin' folder are modified. - -jobs: - unittest: - runs-on: ubuntu-20.04 - strategy: - matrix: - python-version: ['3.11'] - steps: - - name: Checkout - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install requirements - run: python -m pip install -r requirements.txt - - name: Run unittests - run: | - PYTHONPATH=bin python -m unittest discover -s bin/tests diff --git a/sources/README.md b/sources/README.md index 53b7bd16..619abf08 100644 --- a/sources/README.md +++ b/sources/README.md @@ -216,6 +216,13 @@ When the tests succeed a maintainer will merge the dev branch into main. Feel fr The reason we are not running the tests directly on the pull request branch is, that this does not allow to access the GitHub secrets, that are required to run the tests. +# Run the unit tests locally + +``` +cd codex/sources +PYTHONPATH=bin python -m unittest discover -s bin/tests +``` + ### Tools To make a test run of the tool to check its functionalities follow [Usage](#Usage) to set-up the environnement and the API key, then run diff --git a/sources/bin/tests/readme.md b/sources/bin/tests/readme.md deleted file mode 100644 index ac40fb36..00000000 --- a/sources/bin/tests/readme.md +++ /dev/null @@ -1,6 +0,0 @@ -# Run the tests locally - -``` -cd codex/sources -PYTHONPATH=bin python -m unittest discover -s bin/tests -``` \ No newline at end of file diff --git a/sources/bin/tests/test_extract_galaxy_workflows.py b/sources/bin/tests/test_extract_galaxy_workflows.py index c35b5974..9d788b2c 100644 --- a/sources/bin/tests/test_extract_galaxy_workflows.py +++ b/sources/bin/tests/test_extract_galaxy_workflows.py @@ -1,10 +1,7 @@ import json import os import unittest -from typing import ( - Any, - Dict, -) +from typing import Dict from unittest.mock import ( MagicMock, patch, @@ -26,7 +23,7 @@ def setUp(self) -> None: json_file_path = os.path.join(self.script_dir, "test-data", "workflowhub_api_mock.json") # Open and load the JSON file - with open(json_file_path, "r") as file: + with open(json_file_path) as file: self.mock_responses = json.load(file) # Define the side effect function